Fwd: CUDA error cudaStreamSynchronize(stream) and CUDA error in ComputeBondedCUDA
I am now wondering whether the nvidia driver, as built automatically by Debian during tecent updating/upgrading, allows correct rendering but fails with NAMD computations To this concern, it is not clear to me whether Debian, with its automatic building, uses the proprietary nvidia driver. If not, I could try by downloading the proprietary nvidia driver -- Forwarded message - From: Francesco Pietra Date: Sun, Nov 20, 2022, 7:07 PM Subject: CUDA error cudaStreamSynchronize(stream) and CUDA error in ComputeBondedCUDA To: debian-users Hello Main board GA-X79-UD3 with two 680 GPUs Debian10 Linux, kernel 5.10.0-19-amd64 OpenGL 4.6.0 nvidia driver 470.141.03 -- Months ago, following updating/upgrading of amd64, the GPUs, while rendering correctly, became unable to run classical molecular dynamics simulations. Launching a minimization with software NAMD with both GPUs or with one of them (by software or even by removing one GPU) namd2 +idlepoll +p12 +devices 0,1 min.conf namd2 +idlepoll +p12 +devices 0 min.conf namd2 +idlepoll +p12 +devices 1 min.conf NAMD organizes the simulation correctly but at the stage of starting the computation, accessing memory, a crash occurs with error TCL: Minimizing for 3000 steps > FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file > src/CudaTileListKernel.cu, function buildTileLists, line 1136 > on Pe 4 (gig64 device 0 pci 0:2:0): an illegal memory access was > encountered > FATAL ERROR: CUDA error in ComputeBondedCUDA::forceDoneCheck after polling > 48 times over 0.005047 s on Pe 8 (gig64 device 1 pci 0:3:0): an illegal > memory access was encountered > FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file > src/CudaTileListKernel.cu, function buildTileLists, line 1136 > on Pe 4 (gig64 device 0 pci 0:2:0): an illegal memory access was > encountered > FATAL ERROR: CUDA error in ComputeBondedCUDA::forceDoneCheck after polling > 48 times over 0.005047 s on Pe 8 (gig64 device 1 pci 0:3:0): an illegal > memory access was encountered > [Partition 0][Node 0] End of program > "illegal memory access" is a software error (as also proven by using alternatively one of the two GPUs) that escapes all my attempts at unraveling its origin. I had no clues from NAMD forum. Hope here. Thanks for your kind attention francesco pietra
CUDA error cudaStreamSynchronize(stream) and CUDA error in ComputeBondedCUDA
Hello Main board GA-X79-UD3 with two 680 GPUs Debian10 Linux, kernel 5.10.0-19-amd64 OpenGL 4.6.0 nvidia driver 470.141.03 -- Months ago, following updating/upgrading of amd64, the GPUs, while rendering correctly, became unable to run classical molecular dynamics simulations. Launching a minimization with software NAMD with both GPUs or with one of them (by software or even by removing one GPU) namd2 +idlepoll +p12 +devices 0,1 min.conf namd2 +idlepoll +p12 +devices 0 min.conf namd2 +idlepoll +p12 +devices 1 min.conf NAMD organizes the simulation correctly but at the stage of starting the computation, accessing memory, a crash occurs with error TCL: Minimizing for 3000 steps > FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file > src/CudaTileListKernel.cu, function buildTileLists, line 1136 > on Pe 4 (gig64 device 0 pci 0:2:0): an illegal memory access was > encountered > FATAL ERROR: CUDA error in ComputeBondedCUDA::forceDoneCheck after polling > 48 times over 0.005047 s on Pe 8 (gig64 device 1 pci 0:3:0): an illegal > memory access was encountered > FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file > src/CudaTileListKernel.cu, function buildTileLists, line 1136 > on Pe 4 (gig64 device 0 pci 0:2:0): an illegal memory access was > encountered > FATAL ERROR: CUDA error in ComputeBondedCUDA::forceDoneCheck after polling > 48 times over 0.005047 s on Pe 8 (gig64 device 1 pci 0:3:0): an illegal > memory access was encountered > [Partition 0][Node 0] End of program > "illegal memory access" is a software error (as also proven by using alternatively one of the two GPUs) that escapes all my attempts at unraveling its origin. I had no clues from NAMD forum. Hope here. Thanks for your kind attention francesco pietra
CUDA error illegal memory access
With debian 11 bullseye I encounter illegal mem access when trying to carry out molecular dynamics on two GTX 680. On the same linux box no such error was encountered with debian 10. The error arose with upgrading to 11' Thanks for advice FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function buildTileLists, line 1136 on Pe 4 (gig64 device 0 pci 0:2:0): an illegal memory access was encountered FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function buildTileLists, line 1136 on Pe 4 (gig64 device 0 pci 0:2:0): an illegal memory access was encountered [Partition 0][Node 0] End of program FATAL ERROR: CUDA error cudaMalloc(pp, sizeofT*(*curlen)) in file src/CudaUtils.C, function reallocate_device_T, line 130 on Pe 8 (gig64 device 1 pci 0:3:0): an illegal memory access was encountered FATAL ERROR: CUDA error cudaMalloc(pp, sizeofT*(*curlen)) in file src/CudaUtils.C, function reallocate_device_T, line 130 on Pe 8 (gig64 device 1 pci 0:3:0): an illegal memory access was encountered FATAL ERROR: CUDA error in ComputeBondedCUDA::forceDoneCheck after polling 0 times over 0.006701 s on Pe 4 (gig64 device 0 pci 0:2:0): an illegal memory access was encountered FATAL ERROR: CUDA error in ComputeBondedCUDA::forceDoneCheck after polling 0 times over 0.006701 s on Pe 4 (gig64 device 0 pci 0:2:0): an illegal memory access was encountered francesco@gig64:~/work_lissoclimides/C45/sphere35/MD$
Re: AVOGADRO2 plugins howto
Thanks a lot. I had taken another way, frustrated by avogadro, but as soon as possible l'll be back to avogadro with your suggestions On Fri, Mar 4, 2022, 3:18 PM Dan Ritter wrote: > Francesco Pietra wrote: > > Yes 1.93. I read that this is also called avogadro2, but I may be wrong. > > At any event, the real question is how to have working plugins with the > > avogadro version supplied by bullseye > > thanks. Downloading plugins, and then? > > https://plugins.avogadro.cc/ > > Every plugin seems to have its own installation method, but the > most common seems to be: > > move the plugin to > /home//.local/share/OpenChemistry/Avogadro/ > > and run > > python install_plugin.py > /home//.local/share/OpenChemistry/Avogadro/ > > > Overall, this seems to be a remarkably poorly documented system. > > -dsr- >
Re: AVOGADRO2 plugins howto
Yes 1.93. I read that this is also called avogadro2, but I may be wrong. At any event, the real question is how to have working plugins with the avogadro version supplied by bullseye thanks. Downloading plugins, and then? fp On Fri, Mar 4, 2022 at 8:52 AM Dan Ritter wrote: > Francesco Pietra wrote: > > With bullseye avogadro2 requires calling plugins to carry out simple > tasks. > > I was unable to install them. Howto? > > > > If it is a bug, or incomplete package, how to replace avogadro2 with the > > old avogadro? > > bullseye supplies avogadro=1.93 > > The real question, I think, is where did you get avogadro2 from? > > -dsr- >
AVOGADRO2 plugins howto
With bullseye avogadro2 requires calling plugins to carry out simple tasks. I was unable to install them. Howto? If it is a bug, or incomplete package, how to replace avogadro2 with the old avogadro? thanks francesco pietra
Fwd: namd-l: Fwd: nvidia issue with namd12 Debian 11
Was this "illegal mem access" with namd12 resolved? ISSUE* somehow I have a lot of problems with the NAMD-2.12 version. All CUDA jobs * >From * owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu ] *Im * *> Auftrag von *Norman Geist * *> *Gesendet:* Freitag, 10. März 2017 10:16 * *will: **1. Immediately fail for SMP single process runs when having more * *than 1 thread via ++ppn: * *FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file * *src/CudaTileListKernel.cu, function sortTileLists * *on Pe 4 (gpu5 device 1): an illegal memory access was encountered * *- Processor 4 Exiting: Called CmiAbort * *Reason: FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file * *src/CudaTileListKernel.cu, function sortTileLists * *on Pe 4 (gpu5 device 1): an illegal memory access was encountered * *This happens for my own compiled versions (CUDA-7.5) as well as for the * *precompiled multicore version (CUDA-6.5). * *From:* Ajasja Ljubetič (*ajasja.ljubetic_at_gmail.com* ) *Date:* Fri Mar 10 2017 - 05:14:10 CST Are you sure your graphics card is OK? Have you tried any of the available memory checkers? *From:* Norman Geist (*norman.geist_at_uni-greifswald.de* ) *Date:* Fri Mar 10 2017 - 05:41:10 CST Yes, since it works with gromacs, cp2k and namd versions < 2.12. Maybe I should also mention that I’m using amber FF and files. .. Actually, as far as I understand, "illegal mem access" is a software not hardware problem. What could I do? Perhaps running something else than NAMD, may be a game involving the GPUs? Thanks for advice francesco -- Forwarded message - From: Francesco Pietra Date: Mon, Jan 17, 2022 at 3:50 PM Subject: Re: namd-l: Fwd: nvidia issue with namd12 Debian 11 To: Vermaas, Josh Cc: nam...@ks.uiuc.edu , debian-users < debian-user@lists.debian.org> Hi Josh, no big system: Info) Analyzing structure ... Info)Atoms: 107292 Info)Bonds: 77829 Info)Angles: 61441 Dihedrals: 46455 Impropers: 1604 Cross-terms: 158 Info)Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info)Residues: 31152 Info)Waters: 30102 Info)Segments: 128 Info)Fragments: 30587 Protein: 9 Nucleic: 25 Following your hint, I tried MD with a very small system: Info) Analyzing structure ... Info)Atoms: 1448 Info)Bonds: 1187 Info)Angles: 1618 Dihedrals: 699 Impropers: 0 Cross-terms: 0 Info)Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info)Residues: 261 Info)Waters: 0 Info)Segments: 33 Info)Fragments: 261 Protein: 0 Nucleic: 0 Exactly the same error messages that I reported for the bigger system. So, it is not a problem of insufficient mem on the GTX. My very feeble guess is that there is a mismatch between the linux kernel and the nvidia driver, but they were selected by the Debian code and other people should have met the issue. I am not sure that Debian 11 could work correctly with a downgraded couple of linux kernel/nvidia driver. Perhaps it could easier to downgrade to Debian 10, which worked correctly on my raid1 box. thanks francesco Incidentally, I said namd12, while it is 14. On Mon, Jan 17, 2022 at 1:24 PM Vermaas, Josh wrote: > How big is your system? The error being tossed back is that you are out of > memory. The GTX 680 only has 2GB of memory, and so depending on your system > size you may run yourself out of memory. > > > > -Josh > > > > *From: * on behalf of Francesco Pietra < > chiendar...@gmail.com> > *Reply-To: *"nam...@ks.uiuc.edu" , Francesco Pietra < > chiendar...@gmail.com> > *Date: *Monday, January 17, 2022 at 4:40 AM > *To: *NAMD , debian-users < > debian-user@lists.debian.org> > *Subject: *namd-l: Fwd: nvidia issue with namd12 Debian 11 > > > > I forgot to add that commands 'nvidia-detect' and 'nvidia-smi' detect both > GTX 680 as activated and tells that they are supported by all driver > versions, including those for Tesla 450. > > Actually, legacy nvidia drivers are only required for very old nvidia > graphic cards, from 400 downwards. > > > > I alsoo add that the box is at CUDA 11.2 > > > > -- Forwarded message - > From: *Francesco Pietra* > Date: Mon, Jan 17, 2022 at 4:15 AM > Subject: nvidia issue with namd12 Debian 11 > To: NAMD , debian-users > > > > With a Debian 11 box with two GTX 680 I am unable to get them working. The > problem occurred with upgrading from debian 10 to 11 and, from namd 11 to > 12 (/NAMD_Git-2021-11-27_Linux-x86_64-multicore-CUDA) > > > > nvidia-driver 460.91.03-1 > > linux-image-amd64 5.10.84-1 > > linux kernel 5.10.0-10-amd64 > > > > Error when trying a minimization: > > > > TCL: Minimizing
Re: namd-l: Fwd: nvidia issue with namd12 Debian 11
Hi Josh, no big system: Info) Analyzing structure ... Info)Atoms: 107292 Info)Bonds: 77829 Info)Angles: 61441 Dihedrals: 46455 Impropers: 1604 Cross-terms: 158 Info)Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info)Residues: 31152 Info)Waters: 30102 Info)Segments: 128 Info)Fragments: 30587 Protein: 9 Nucleic: 25 Following your hint, I tried MD with a very small system: Info) Analyzing structure ... Info)Atoms: 1448 Info)Bonds: 1187 Info)Angles: 1618 Dihedrals: 699 Impropers: 0 Cross-terms: 0 Info)Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0 Info)Residues: 261 Info)Waters: 0 Info)Segments: 33 Info)Fragments: 261 Protein: 0 Nucleic: 0 Exactly the same error messages that I reported for the bigger system. So, it is not a problem of insufficient mem on the GTX. My very feeble guess is that there is a mismatch between the linux kernel and the nvidia driver, but they were selected by the Debian code and other people should have met the issue. I am not sure that Debian 11 could work correctly with a downgraded couple of linux kernel/nvidia driver. Perhaps it could easier to downgrade to Debian 10, which worked correctly on my raid1 box. thanks francesco Incidentally, I said namd12, while it is 14. On Mon, Jan 17, 2022 at 1:24 PM Vermaas, Josh wrote: > How big is your system? The error being tossed back is that you are out of > memory. The GTX 680 only has 2GB of memory, and so depending on your system > size you may run yourself out of memory. > > > > -Josh > > > > *From: * on behalf of Francesco Pietra < > chiendar...@gmail.com> > *Reply-To: *"nam...@ks.uiuc.edu" , Francesco Pietra < > chiendar...@gmail.com> > *Date: *Monday, January 17, 2022 at 4:40 AM > *To: *NAMD , debian-users < > debian-user@lists.debian.org> > *Subject: *namd-l: Fwd: nvidia issue with namd12 Debian 11 > > > > I forgot to add that commands 'nvidia-detect' and 'nvidia-smi' detect both > GTX 680 as activated and tells that they are supported by all driver > versions, including those for Tesla 450. > > Actually, legacy nvidia drivers are only required for very old nvidia > graphic cards, from 400 downwards. > > > > I alsoo add that the box is at CUDA 11.2 > > > > -- Forwarded message - > From: *Francesco Pietra* > Date: Mon, Jan 17, 2022 at 4:15 AM > Subject: nvidia issue with namd12 Debian 11 > To: NAMD , debian-users > > > > With a Debian 11 box with two GTX 680 I am unable to get them working. The > problem occurred with upgrading from debian 10 to 11 and, from namd 11 to > 12 (/NAMD_Git-2021-11-27_Linux-x86_64-multicore-CUDA) > > > > nvidia-driver 460.91.03-1 > > linux-image-amd64 5.10.84-1 > > linux kernel 5.10.0-10-amd64 > > > > Error when trying a minimization: > > > > TCL: Minimizing for 3000 steps > FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file > src/CudaTileListKernel.cu, function sortTileLists, line 1577 > on Pe 2 (gig64 device 0 pci 0:2:0): an illegal memory access was > encountered > FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file > src/CudaTileListKernel.cu, function sortTileLists, line 1577 > on Pe 2 (gig64 device 0 pci 0:2:0): an illegal memory access was > encountered > [Partition 0][Node 0] End of program > FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file > src/CudaTileListKernel.cu, function sortTileLists, line 1577 > on Pe 4 (gig64 device 1 pci 0:3:0): an illegal memory access was > encountered > FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file > src/CudaTileListKernel.cu, function sortTileLists, line 1577 > on Pe 4 (gig64 device 1 pci 0:3:0): an illegal memory access was > encountered > > > > I have also reconfigured the xserver, at no avail. > > > > I have noticed issues about namd12/nvidia on the web, apparently > unresolved. > > > > Thanks for advice > > francesco pietra > > > > >
Fwd: nvidia issue with namd12 Debian 11
I forgot to add that commands 'nvidia-detect' and 'nvidia-smi' detect both GTX 680 as activated and tells that they are supported by all driver versions, including those for Tesla 450. Actually, legacy nvidia drivers are only required for very old nvidia graphic cards, from 400 downwards. I alsoo add that the box is at CUDA 11.2 -- Forwarded message - From: Francesco Pietra Date: Mon, Jan 17, 2022 at 4:15 AM Subject: nvidia issue with namd12 Debian 11 To: NAMD , debian-users With a Debian 11 box with two GTX 680 I am unable to get them working. The problem occurred with upgrading from debian 10 to 11 and, from namd 11 to 12 (/NAMD_Git-2021-11-27_Linux-x86_64-multicore-CUDA) nvidia-driver 460.91.03-1 linux-image-amd64 5.10.84-1 linux kernel 5.10.0-10-amd64 Error when trying a minimization: TCL: Minimizing for 3000 steps FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function sortTileLists, line 1577 on Pe 2 (gig64 device 0 pci 0:2:0): an illegal memory access was encountered FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function sortTileLists, line 1577 on Pe 2 (gig64 device 0 pci 0:2:0): an illegal memory access was encountered [Partition 0][Node 0] End of program FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function sortTileLists, line 1577 on Pe 4 (gig64 device 1 pci 0:3:0): an illegal memory access was encountered FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function sortTileLists, line 1577 on Pe 4 (gig64 device 1 pci 0:3:0): an illegal memory access was encountered I have also reconfigured the xserver, at no avail. I have noticed issues about namd12/nvidia on the web, apparently unresolved. Thanks for advice francesco pietra
nvidia issue with namd12 Debian 11
With a Debian 11 box with two GTX 680 I am unable to get them working. The problem occurred with upgrading from debian 10 to 11 and, from namd 11 to 12 (/NAMD_Git-2021-11-27_Linux-x86_64-multicore-CUDA) nvidia-driver 460.91.03-1 linux-image-amd64 5.10.84-1 linux kernel 5.10.0-10-amd64 Error when trying a minimization: TCL: Minimizing for 3000 steps FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function sortTileLists, line 1577 on Pe 2 (gig64 device 0 pci 0:2:0): an illegal memory access was encountered FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function sortTileLists, line 1577 on Pe 2 (gig64 device 0 pci 0:2:0): an illegal memory access was encountered [Partition 0][Node 0] End of program FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function sortTileLists, line 1577 on Pe 4 (gig64 device 1 pci 0:3:0): an illegal memory access was encountered FATAL ERROR: CUDA error cudaStreamSynchronize(stream) in file src/CudaTileListKernel.cu, function sortTileLists, line 1577 on Pe 4 (gig64 device 1 pci 0:3:0): an illegal memory access was encountered I have also reconfigured the xserver, at no avail. I have noticed issues about namd12/nvidia on the web, apparently unresolved. Thanks for advice francesco pietra
netwok issues
Replaced defective Tyan-double-opterons server mainboard with a minimal asus H81M-K-intel i3, maintaining the same two mirror-raid HDs with debian amd64 wheezy. Now, network is only establised at a ZyXEL router when loading gnome, thereafter slogin to my amd64 server occurs regularly. Before that, at the linux prompt, no network with the H81M-K. Command # dhclient also fails to establish network. Thanks for suggesting where correcting. francesco pietra
Re: Debian installer and raid0
Hello: I know that a correct software mirror raid is subject to failures, when anything wrong is written to both disks. And I also know that hardware mirror raid is subject to hardware failures. I said at the beginning that I keep two wheezy mirror-raid servers with the same data and software. Now that mirror raid in all my machines is fully in order (also thanks to you) I maintain three wheezy servers in the same situation (I recovered what had been set aside in order to have three different jobs going on). That is multiple backup. I can switch disks from one to another one. Very large data files are at the supercomputer center, where multiple backup is also carried out. As to inexpensive ssh access to my machines and supercomputer center, I use a cheap tablet, equipped with a physical US keyboard, where I installed a minimal linux (ssh, text editor, browser). That allows continuous access under a negligible electricity bill. Thanks again for all your help francesco PS: You did not comment whether the pipe' command that I use to verify grub has a general validity. As far as I could use it, I found it equivalent to examining each disk, one at a time. Cheers francesco On Sat, Oct 12, 2013 at 11:36 PM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: I hope not to bother beyond the limit, but the security of mirror raid is something of utmost importance, at least in my work of biochemist, with very limited ability in recovering from disk failures. I must express concern. While RAID is very useful to keeping a system running across disk failures that it is not a backup. Even with RAID functioning perfectly it is possible to have accidental file deletion and other file mangling. A known good backup is still required! Having good RAID does not remove the need for a backup. Operating a critical system without backup is a scary thing. Important enough to repeat. A known good backup is still required! Bob
Fwd: Debian installer and raid0
grub installation of lacking grub on the CPU-GPU raid1 machine (gig64) by the command grub-install /dev/sdb was successful (Installation finished. No error reported) with either the two victim 250GB disks and then with the two 1000GB disks. I can't explain my failure to do so in the recent past. The pipe command that I described before proved equivalent to what you described, i.e., physically testing whether grub is installed, each disk at a time. Thanks a lot francesco -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Tue, Oct 8, 2013 at 5:11 PM Subject: Re: Debian installer and raid0 To: debian-users debian-user@lists.debian.org, amd64 Debian debian-am...@lists.debian.org I hope not to bother beyond the limit, but the security of mirror raid is something of utmost importance, at least in my work of biochemist, with very limited ability in recovering from disk failures. I planned to use the double-opteron, two sockets, server, tya 64, as a victim for the test you suggested. However, the test root@tya64:/home/francesco# dd bs=512 count=1 if=/dev/sda 2/dev/null | strings ZRr= `|f \|f1 GRUB Geom Hard Disk Read Error root@tya64:/home/francesco# dd bs=512 count=1 if=/dev/sdb 2/dev/null | strings ZRr= `|f \|f1 GRUB Geom Hard Disk Read Error suggested that grub was installed on both disks. Using one disk at a time, as you suggested, was in accordance. Then I carried out the pipe test with the recent machine, gig64: root@gig64:/home/francesco# dd bs=512 count=1 if=/dev/sda 2/dev/null | strings ZRr= `|f \|f1 GRUB Geom Hard Disk Read Error root@gig64:/home/francesco# dd bs=512 count=1 if=/dev/sdb 2/dev/null | strings root@gig64:/home/francesco# indicating that grub is installed on sda only. Confirmed by using one disk at a time. 500GB disks on tya64 came from a dismissed doubleOpteron four socket server that I had assembled several years ago. Probably at that time in my activity as a biochemist I was left more time to be careful about linux. With gig64 the two 1000GB disks came recently from the store and the described failure as to installing grub on sdb was with them. Unless the problem is different, related to the particular gig64 machine. QUESTIONS: (1) If there is any chance that the particular hardware of gig64, comprising two GPUs (I called gig64 a server, while, unlike the real server tya64, it is a consumer mainboard GA-X79-UD3 with Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz and two GTX680 GPUs, leading to very fast number crunching, NOT overclocked) can interfere with installation of grub on the second disk, it seems to me that gig64 is the appropriate victim. However, by replacing the two 1000GB disks with two spare victim disks that I should have somewhere (amd64 on both, and likely grub too). If anything, linux is unable to tell anything about the GPUs (and even nvidia-smi tools tell very little, which my lend suspicion on why the grub installation of the second disk failed). Fundamentally, it is a game machine, so that no chance to get mirror raid even mentioned by bloggers of this type of computers. (2) Is the above pipe test (that grub installed leads to some message when failure is encountered, while no message means no grub available) always reliable and equivalent to detaching disks? thanks francesco On Mon, Oct 7, 2013 at 10:38 PM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: I forgot asking naively how to boot safely to the grub menu. Press a key on the keyboard before the 5 second count down timer counts all of the way down. Pressing a key stops the timer and causes it to stay on the menu waiting for keyboard input. Bob
Re: Debian installer and raid0
I hope not to bother beyond the limit, but the security of mirror raid is something of utmost importance, at least in my work of biochemist, with very limited ability in recovering from disk failures. I planned to use the double-opteron, two sockets, server, tya 64, as a victim for the test you suggested. However, the test root@tya64:/home/francesco# dd bs=512 count=1 if=/dev/sda 2/dev/null | strings ZRr= `|f \|f1 GRUB Geom Hard Disk Read Error root@tya64:/home/francesco# dd bs=512 count=1 if=/dev/sdb 2/dev/null | strings ZRr= `|f \|f1 GRUB Geom Hard Disk Read Error suggested that grub was installed on both disks. Using one disk at a time, as you suggested, was in accordance. Then I carried out the pipe test with the recent machine, gig64: root@gig64:/home/francesco# dd bs=512 count=1 if=/dev/sda 2/dev/null | strings ZRr= `|f \|f1 GRUB Geom Hard Disk Read Error root@gig64:/home/francesco# dd bs=512 count=1 if=/dev/sdb 2/dev/null | strings root@gig64:/home/francesco# indicating that grub is installed on sda only. Confirmed by using one disk at a time. 500GB disks on tya64 came from a dismissed doubleOpteron four socket server that I had assembled several years ago. Probably at that time in my activity as a biochemist I was left more time to be careful about linux. With gig64 the two 1000GB disks came recently from the store and the described failure as to installing grub on sdb was with them. Unless the problem is different, related to the particular gig64 machine. QUESTIONS: (1) If there is any chance that the particular hardware of gig64, comprising two GPUs (I called gig64 a server, while, unlike the real server tya64, it is a consumer mainboard GA-X79-UD3 with Intel(R) Core(TM) i7-3930K CPU @ 3.20GHz and two GTX680 GPUs, leading to very fast number crunching, NOT overclocked) can interfere with installation of grub on the second disk, it seems to me that gig64 is the appropriate victim. However, by replacing the two 1000GB disks with two spare victim disks that I should have somewhere (amd64 on both, and likely grub too). If anything, linux is unable to tell anything about the GPUs (and even nvidia-smi tools tell very little, which my lend suspicion on why the grub installation of the second disk failed). Fundamentally, it is a game machine, so that no chance to get mirror raid even mentioned by bloggers of this type of computers. (2) Is the above pipe test (that grub installed leads to some message when failure is encountered, while no message means no grub available) always reliable and equivalent to detaching disks? thanks francesco On Mon, Oct 7, 2013 at 10:38 PM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: I forgot asking naively how to boot safely to the grub menu. Press a key on the keyboard before the 5 second count down timer counts all of the way down. Pressing a key stops the timer and causes it to stay on the menu waiting for keyboard input. Bob
Re: Debian installer and raid0
I have no other machines than the said two servers. As soon as a machine was dismissed, parts were recovered for the new machines. Does not matter, I'll try. What I was also asking, however, was how to boot to the grub only: I forgot asking naively how to boot safely to the grub menu. With both servers, the system boots straightforwardly to the linux prompt, then, if I need the X server and manager, I command startx and then gnome-session thanks francesco On Sun, Oct 6, 2013 at 10:40 PM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: Thanks so much. I am also using raid1 since I met Debian, so many years ago. However the poor way I described. I'll do what you suggest as soon time permits, although the cables to the HDs in the old server are difficultly accessible. And, in the meantime, I would be at a single server, insecure as with a bad raid1. I wasn't suggesting that you hack around on your production server. I was suggesting that you create a victim machine for testing on a workbench that is seperate from your production server. And this victim machine does not need to be a rack mount server at all. An old deskside machine is perfect. Something that has two disk drives in it for testing the RAID1 installation. Do the test on this testing victim machine separate from your production machine. When you have verified how everything works then do those actions on your production machine. That way your production machine is safe from experiments. And it is much easier to test and learn and experiment upon a machine that is targeted specifically for that purpose. Failure that I described in adding grub to the other HD was in a single trial and now the HDs are different, taken from a dismissed four-sockets dual-core AMD server. The type of disk drive should not matter. Bob
Re: Debian installer and raid0
Thanks so much. I am also using raid1 since I met Debian, so many years ago. However the poor way I described. I'll do what you suggest as soon time permits, although the cables to the HDs in the old server are difficultly accessible. And, in the meantime, I would be at a single server, insecure as with a bad raid1. Failure that I described in adding grub to the other HD was in a single trial and now the HDs are different, taken from a dismissed four-sockets dual-core AMD server. cheers francesco On Fri, Oct 4, 2013 at 10:13 PM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: Bob Proulx wrote: After installing simply run the grub install script against both disks manually and then you will be assured that it has been installed on both disks. I had problems with that methodology and was unable to detect my error. From a thread on debian dated Mar 2, 2013: ... grub-install /dev/sdb was reported by complete installation. No error, no warning. On rebooting, GRUB was no more found. Then entering in grub rescue prefix/root/ were now wrong. If the command does not work on the command line then it won't work from the installer either. The installer is doing the same things that you can do from the command line. Therefore asking if it is in the installer won't help. Because if it doesn't work then it doesn't work either place. If it does work then it will work either place. That is my conjecture at least. And since I have been using this feature I believe it does work. Works for me anyway. I have been using RAID1 for a long time and have not encountered the problem you describe. That doesn't mean that such an error doesn't occur. Just that I can't recreate it. Or rather after much user have never recreated it. This applies to both the good grub version 1 as well as the newer and IMNHO buggier grub version 2 rewrite. They are completely different from each other. Statements made about one do not apply to the other because it was a complete rewrite. But it is certainly possible that in your configuration that you have a case that does not work. I have a workbench with a variety of hardware. When I want to test something like this I construct a victim system in which to try the action. If you could do the same I think it would help to get to the root cause of the problem. I would create a victim machine with two drives for installation testing. Then test the installation. After install and reboot then shutdown, unplug one disk, test boot. Do not boot all of the way to the system. Simply boot to the grub menu and stop there. Then power off, switch disks, and test boot again. Do not boot all of the way to the system. Simply boot to the grub menu and again stop there. If you can get to the grub menu from either disk then grub has been installed on both disks. If not then plug both disks in and boot the system and test the grub-install script on the non-booting disk and then repeat the single disk boot. The reason to only boot to the grub menu is of course so that the RAID1 doesn't get split. If booting with one disk and then the other one disk it will get a split brain of course. No real problem on a victim machine. But it is faster to keep them in sync. So I only boot to the grub menu when testing the grub boot code. Avoiding booting the system avoids splitting the raid unnecessarily and speeds up the debugging. By testing this way you can verify that you can boot either disk in isolation after the other disk has failed. By using a victim machine you can experiment. Then if you find a bug you will have a recipe to recreate it and can file a bug report on it. Being able to recreate the problem is the most valuable part. And here is the challenge. I think if you do this you will find that it does actually work. But feel free to write back here and tell me that I am wrong and that there is a problem with it. :-) As the great Mark Twain wrote There is nothing so annoying as a good example. If you can get to a repeatable test case that fails that would be awesome. Now I am in the same situation, two servers with mirroring raid, grub on /dev/sda only. Identical data on both servers to cope with grub on one disk only. Not smart from my side. Two servers so that you can switch your services from one server to the other in case one of the servers cannot boot? If you have two servers and one is the hot spare for the other then perhaps after doing your own victim machine testing then you can perform the fix on the spare and test there. Then apply the fix to the running server. I think that should be a safe way to sneak up on the solution. Bob
Fwd: Debian installer and raid0
I forgot asking naively how to boot safely to the grub menu. With both servers, the system boots straightforwardly to the linux prompt, then, if I need the X server and manager, I command startx and then gnome-session thanks francesco -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Sat, Oct 5, 2013 at 9:21 AM Subject: Re: Debian installer and raid0 To: debian-users debian-user@lists.debian.org, amd64 Debian debian-am...@lists.debian.org Thanks so much. I am also using raid1 since I met Debian, so many years ago. However the poor way I described. I'll do what you suggest as soon time permits, although the cables to the HDs in the old server are difficultly accessible. And, in the meantime, I would be at a single server, insecure as with a bad raid1. Failure that I described in adding grub to the other HD was in a single trial and now the HDs are different, taken from a dismissed four-sockets dual-core AMD server. cheers francesco On Fri, Oct 4, 2013 at 10:13 PM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: Bob Proulx wrote: After installing simply run the grub install script against both disks manually and then you will be assured that it has been installed on both disks. I had problems with that methodology and was unable to detect my error. From a thread on debian dated Mar 2, 2013: ... grub-install /dev/sdb was reported by complete installation. No error, no warning. On rebooting, GRUB was no more found. Then entering in grub rescue prefix/root/ were now wrong. If the command does not work on the command line then it won't work from the installer either. The installer is doing the same things that you can do from the command line. Therefore asking if it is in the installer won't help. Because if it doesn't work then it doesn't work either place. If it does work then it will work either place. That is my conjecture at least. And since I have been using this feature I believe it does work. Works for me anyway. I have been using RAID1 for a long time and have not encountered the problem you describe. That doesn't mean that such an error doesn't occur. Just that I can't recreate it. Or rather after much user have never recreated it. This applies to both the good grub version 1 as well as the newer and IMNHO buggier grub version 2 rewrite. They are completely different from each other. Statements made about one do not apply to the other because it was a complete rewrite. But it is certainly possible that in your configuration that you have a case that does not work. I have a workbench with a variety of hardware. When I want to test something like this I construct a victim system in which to try the action. If you could do the same I think it would help to get to the root cause of the problem. I would create a victim machine with two drives for installation testing. Then test the installation. After install and reboot then shutdown, unplug one disk, test boot. Do not boot all of the way to the system. Simply boot to the grub menu and stop there. Then power off, switch disks, and test boot again. Do not boot all of the way to the system. Simply boot to the grub menu and again stop there. If you can get to the grub menu from either disk then grub has been installed on both disks. If not then plug both disks in and boot the system and test the grub-install script on the non-booting disk and then repeat the single disk boot. The reason to only boot to the grub menu is of course so that the RAID1 doesn't get split. If booting with one disk and then the other one disk it will get a split brain of course. No real problem on a victim machine. But it is faster to keep them in sync. So I only boot to the grub menu when testing the grub boot code. Avoiding booting the system avoids splitting the raid unnecessarily and speeds up the debugging. By testing this way you can verify that you can boot either disk in isolation after the other disk has failed. By using a victim machine you can experiment. Then if you find a bug you will have a recipe to recreate it and can file a bug report on it. Being able to recreate the problem is the most valuable part. And here is the challenge. I think if you do this you will find that it does actually work. But feel free to write back here and tell me that I am wrong and that there is a problem with it. :-) As the great Mark Twain wrote There is nothing so annoying as a good example. If you can get to a repeatable test case that fails that would be awesome. Now I am in the same situation, two servers with mirroring raid, grub on /dev/sda only. Identical data on both servers to cope with grub on one disk only. Not smart from my side. Two servers so that you can switch your services from one server to the other in case one of the servers cannot boot? If you have two servers and one
Re: Debian installer and raid0
recall that it has been added with Wheezy. But let me put forward that it doesn't really matter. If you have RAID then you know you want grub on both disks. After installing simply run the grub install script against both disks manually and then you will be assured that it has been installed on both disks. I had problems with that methodology and was unable to detect my error. From a thread on debian dated Mar 2, 2013: I carried out a reinstall of amd64 wheezy on the machine with new HD. md0 (boot, ext20, md1 (LVM, home, usr, etc). GRUB came installed on /dev/sda only Then the command grub-install /dev/sdb was reported by complete installation. No error, no warning. On rebooting, GRUB was no more found. Then entering in grub rescue prefix/root/ were now wrong. Now I am in the same situation, two servers with mirroring raid, grub on /dev/sda only. Identical data on both servers to cope with grub on one disk only. Not smart from my side. I agree with the other responder. It is unlikely IMNHO that you want RAID0 (striping) for the system disk. You most likely want RAID1 (mirroring) instead. The answer above is the same regardless. If you are thinking striping for performance instead I recommend using an SSD for the system disk. Ah! my mistake. Sure, raid1 (mirroring) thanks francesco On Fri, Oct 4, 2013 at 12:22 AM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: Did you use a recent version of the installer? What I would like to know - before reinstalling everything on my servers - is whether the option to set grub on both disks of raid 0 has now been introduced. I recall that it has been added with Wheezy. But let me put forward that it doesn't really matter. If you have RAID then you know you want grub on both disks. After installing simply run the grub install script against both disks manually and then you will be assured that it has been installed on both disks. I agree with the other responder. It is unlikely IMNHO that you want RAID0 (striping) for the system disk. You most likely want RAID1 (mirroring) instead. The answer above is the same regardless. If you are thinking striping for performance instead I recommend using an SSD for the system disk. Bob
Debian installer and raid0
Hello: Did you use a recent version of the installer? What I would like to know - before reinstalling everything on my servers - is whether the option to set grub on both disks of raid 0 has now been introduced. Thanks francesco pietra
Re: RAID1 all bootable
Hello: I started this thread not because grub on both disks should be by default but because I found difficulties in recovering. If I performed badly, and there is no problem in installing grub on the working disk, then I see no problem. There are many raids, not limited to raid1. Perhaps it is because of this that there is no default for raid1. fp On Tue, Jun 4, 2013 at 5:16 AM, Bob Proulx b...@proulx.com wrote: Alexandru Cardaniuc wrote: I just did 2 reinstalls in the last two weeks (upgrade from sqeeze to wheezy screwed up my grub config and then my 6 year old drives started failing - so much fun :), but basically during both reinstalls and creating MD devices with debian installer (md0/md1/md2) using two drives sda/sdb, by default the installer just installed grub on MBR of the first device sda. I didn't see an option to install it everywhere. So, after reboot I did a manual # grub-install /dev/sda # grub-install /dev/sdb Now when I choose to boot from either first disk or second disk, it works fine. Did I miss something during the debian installation? Why wasn't grub automatically installed on both disks? Seems like it should have been. I would file a bug against the debian-installer or installation-reports. Bob
Re: Debian-Linux ally of workstations
Hi Teemu: Thanks for the most useful information. To make the story short, could you point out - from the huge assembly you likked to - a specific device that incorporates a monitor sufficiently wide and well resolved to read papers from scientific journals? And listen to discussions. In current terms, a tablet, however one that could successfully be adapted to Debian or Ubuntu. In the meantime, I came across a discussion that Ubuntu is looking for a hardware company to launch a high-end Ubuntu-based tablet. It could take time, even if true. All the best, francesco On Thu, May 2, 2013 at 3:06 PM, Teemu Ikonen tpiko...@gmail.com wrote: On Wed, May 1, 2013 at 8:38 AM, Francesco Pietra chiendar...@gmail.comwrote: I was looking for some sort of i-device that could allow whifi, directed to reading-downloading literature and be capable of talking - via ssh/scp - with my workstations on a local network (not necessarily wireless). You are probably looking for something which also fits the hardware requirements of the Freedombox project. There's a wiki page of potential hardware here: https://wiki.debian.org/FreedomBox/TargetedHardware In addition to the list above, there's a legion of cheap Android-based mini-pcs available now, most of which can be made to run Debian / Ubuntu at least somehow. The up-to date specs seem to be two 1+ GHz cores, 1 GB memory and 2-8 GBs of flash storage, plus USB, Wifi and ethernet. The SOCs they are based are Allwinner A10/A20, Rockchip RK3066 and AML8726, and probably others. See here for a good selection: http://dx.com/c/consumer-electronics-199/hd-media-players-103/android-hd-players-191 Best, Teemu
Debian-Linux ally of workstations
I was looking for some sort of i-device that could allow whifi, directed to reading-downloading literature and be capable of talking - via ssh/scp - with my workstations on a local network (not necessarily wireless). I have been elsewhere suggested Raspberry, which is Debian GNU-Linux driven, although it focuses on the low price and, therefore, it offers modest performance. Probably inadequate to the task. Also impractical, as it has no integrated monitor, and HDMI port only (no VGA), which, per se, swamps out the low price. Thanks for suggesting a more appropriate i-device. francesco pietra
Re: java on wheezy
On Sun, Apr 14, 2013 at 11:34 PM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: Is any official (= working) advice on getting java at work with wheezy (specifically in amd64, if relevant)? http://wiki.debian.org/Java What should be installed/reconfigured/uninstalled other than the packages obtained from wheezy desktop install, followed by upgrading with deb http://mozilla.debian.net/ experimental iceweasel-beta I am not using iceweasel from experimental. But I am using the same version from Backports on Stable Squeeze 6. Works for me. What is the output of this for you? $ update-alternatives --display mozilla-javaplugin.so mozilla-javaplugin.so - auto mode link currently points to /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so - priority 1071 Current 'best' version is '/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so'. It matches your output: francesco@tya64:~$ update-alternatives --display mozilla-javaplugin.so mozilla-javaplugin.so - auto mode link currently points to /usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so /usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so - priority 1061 Current 'best' version is '/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so'. francesco@tya64:~$ $ dlocate /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so icedtea-7-plugin:amd64: /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so For me (I use v 6): francesco@tya64:~$ dlocate /usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so icedtea-6-plugin:amd64: /usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so francesco@tya64:~$ The above from my machine shows that it is handled by the icedtea-7-plugin:amd64 package. many other javascripts... Note that Java != Javascript. The name Javascript was simply an attempt to ride on the wave of marketing for Java. It has worked. Many people think they are related. They are not. I am not playing with java (useless in the scientific area), however many molecular structures are shown on the web which require java. The world of Java seems fraught with programs that are version specific. Perhaps you are hitting one of those cases. Perhaps Java in general is working but a particular program is version specific and doesn't match your version? Bob: You hit the point. Now, at least from academic centers, I can see all the molecular structures that require java. Thanks for the lesson francesco Bob
java on wheezy
Is any official (= working) advice on getting java at work with wheezy (specifically in amd64, if relevant)? What should be installed/reconfigured/uninstalled other than the packages obtained from wheezy desktop install, followed by upgrading with deb http://mozilla.debian.net/ experimental iceweasel-beta e.g., with my amd64 wheezy installation: java-common openjdk-6-jre libservlet2.5-java icedtea-netx default-jre default-jre-headless libatk-wrapper-java libxz-java libatk-wapper-java-jini libreoffice-java-common libdb-je-java libdb-java libdb5.1-java libdb5.1-java-jini libcommons-beanutils-java libcommons-digester-java libregexp-java libjline-java openjdk-6-jre-headless libxalan2-java liblucene2-java tzdata-java icedtea-netx-common icedtea-6-plugin libhsqldb-java libjtidy-java libcu4j-java ca-certificates-java ant libcommons-logging-java ant-optional libcommons-collections3-java libreoffice-base libcommons-parent-java libgtksourceview-3.0-commor 3.4.2-1 libxml-commons-resolver1.1- 1.2-7 libxml-commons-external-java 1.4.01-2 virtuoso-opensource-6.1-bin libvirtodbc0 virtuoso-opensource-6.1-com jmol vitruoso-minimal libdbus-1-3 dbus many other javascripts... gjs libseed-gtk3-0 libmozjs10d I am not playing with java (useless in the scientific area), however many molecular structures are shown on the web which require java. Thanks francesco pietra
Linking lapack and C standard library
Hello May I ask how to correctly link lapack and C standard libraries with Debian amd64 wheezy? Packages installed: liblapack3gf liblapack3 libblas3 libc6 libc6-dev ** The code to compile makes a generic example: LIBS=-llapack -lstdc++ thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmukjyv54+r5d5534jh+-hjuhpgbs+rggav0m1kd0yz...@mail.gmail.com
Re: Linking lapack and C standard library
Hello João Luis: Sorry for my lack of care in setting the addresses. What I did was: install liblapack3gf-dev to complete the installations, according to previous suggestions. Now, my guess for the link is LIBS=-L/usr/lib -llapack -L/usr/lib -lstdc++ According to the README, a link to both lapack and lstc++ libraries is needed. No link to the C++ compiler, as the above link is for a plugin for a program that is C++ compiled. Should those LIBS above not be correctly linked, the program complises without the plugin. I am going to try with the above link. If it works, I have to consider whether faster libraries would speed up the plugin. I don't know how heavy the mathematical computations are. I have the MKL libraries, though as rpm package. And since a few years, alien alone is no more capable of transforming that rpm to deb. Probably rpm would install with Debian, though one never knows where the files are. Thanks francesco On Thu, Mar 14, 2013 at 1:19 PM, João Luis Meloni Assirati assir...@nonada.if.usp.br wrote: Em 14-03-2013 08:54, Francesco Pietra escreveu: Please see my previous answer, and action. Directions how to compile that program tell that links to both lapack and lstc++ libraries are required in LIBS=. No link to the C++ compiler is required. Francesco, please answer to the list. I could not see your previous answer nor action. I'm a subscriber of the debian-users list only. João Luis. francesco On Thu, Mar 14, 2013 at 12:21 PM, João Luis Meloni Assirati assir...@nonada.if.usp.br wrote: Em 14-03-2013 08:00, Francesco Pietra escreveu: Hello May I ask how to correctly link lapack and C standard libraries with Debian amd64 wheezy? You mean how to compile a C program, linking both lapack and the standard C library to it? I suppose so in the following. Packages installed: liblapack3gf liblapack3 libblas3 libc6 libc6-dev ** You probably need liblapack-dev also, which contains the header files needed to compile our program. The code to compile makes a generic example: LIBS=-llapack -lstdc++ If it's a C program, you don't need the C++ standard library. Suppose your program is a file program.c. Try gcc -llapack -lm -o program program.c Usually you don't have to explicitly link the standard C library (because it is standard), except the math portions of it (so use the -lm switch if you are using math functions from the standard lib). thanks francesco pietra João Luis. -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmuhw+np+yxdmtsymqz5zk6fw7wm+p5viq6-1xmvps7...@mail.gmail.com
Fwd: Linking lapack and C standard library
No, it is not correct. With the indicated links, patching reports all correct Hunk(s), while a post script is incorrect. So that make depends for the program+plugin does not correlate anything. I tried the link to -L/usr with same error. It is not clear to me whether it is a problem of path, or of lacking headers. While I see the headers for stdc++ (commanding locate ..., I don't see headers for lapack (having installed liblapack3gf-dev). Perhaps some other lapack package is required. I tried to have a more verbose patching, as the error indicated both on patching and on make depends: plugin.inc:39: *** missing separator. Stop DONE! does not point to a remedy. francesco -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Thu, Mar 14, 2013 at 3:54 PM Subject: Re: Linking lapack and C standard library To: João Luis Meloni Assirati assir...@nonada.if.usp.br, amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org Hello João Luis: Sorry for my lack of care in setting the addresses. What I did was: install liblapack3gf-dev to complete the installations, according to previous suggestions. Now, my guess for the link is LIBS=-L/usr/lib -llapack -L/usr/lib -lstdc++ According to the README, a link to both lapack and lstc++ libraries is needed. No link to the C++ compiler, as the above link is for a plugin for a program that is C++ compiled. Should those LIBS above not be correctly linked, the program complises without the plugin. I am going to try with the above link. If it works, I have to consider whether faster libraries would speed up the plugin. I don't know how heavy the mathematical computations are. I have the MKL libraries, though as rpm package. And since a few years, alien alone is no more capable of transforming that rpm to deb. Probably rpm would install with Debian, though one never knows where the files are. Thanks francesco On Thu, Mar 14, 2013 at 1:19 PM, João Luis Meloni Assirati assir...@nonada.if.usp.br wrote: Em 14-03-2013 08:54, Francesco Pietra escreveu: Please see my previous answer, and action. Directions how to compile that program tell that links to both lapack and lstc++ libraries are required in LIBS=. No link to the C++ compiler is required. Francesco, please answer to the list. I could not see your previous answer nor action. I'm a subscriber of the debian-users list only. João Luis. francesco On Thu, Mar 14, 2013 at 12:21 PM, João Luis Meloni Assirati assir...@nonada.if.usp.br wrote: Em 14-03-2013 08:00, Francesco Pietra escreveu: Hello May I ask how to correctly link lapack and C standard libraries with Debian amd64 wheezy? You mean how to compile a C program, linking both lapack and the standard C library to it? I suppose so in the following. Packages installed: liblapack3gf liblapack3 libblas3 libc6 libc6-dev ** You probably need liblapack-dev also, which contains the header files needed to compile our program. The code to compile makes a generic example: LIBS=-llapack -lstdc++ If it's a C program, you don't need the C++ standard library. Suppose your program is a file program.c. Try gcc -llapack -lm -o program program.c Usually you don't have to explicitly link the standard C library (because it is standard), except the math portions of it (so use the -lm switch if you are using math functions from the standard lib). thanks francesco pietra João Luis. -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmupspmkrr+bjcp4zeld3+p8n2z+r0xsnrzx9-qirus...@mail.gmail.com
Fwd: Linking lapack and C standard library
As to the problem of linking lapack, I wonder whether this is because it deal of a C-language code, requiring a fine-tuned calling. Is any C interface to lapack in Debian? thanks francesco -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Thu, Mar 14, 2013 at 6:35 PM Subject: Fwd: Linking lapack and C standard library To: amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org No, it is not correct. With the indicated links, patching reports all correct Hunk(s), while a post script is incorrect. So that make depends for the program+plugin does not correlate anything. I tried the link to -L/usr with same error. It is not clear to me whether it is a problem of path, or of lacking headers. While I see the headers for stdc++ (commanding locate ..., I don't see headers for lapack (having installed liblapack3gf-dev). Perhaps some other lapack package is required. I tried to have a more verbose patching, as the error indicated both on patching and on make depends: plugin.inc:39: *** missing separator. Stop DONE! does not point to a remedy. francesco -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Thu, Mar 14, 2013 at 3:54 PM Subject: Re: Linking lapack and C standard library To: João Luis Meloni Assirati assir...@nonada.if.usp.br, amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org Hello João Luis: Sorry for my lack of care in setting the addresses. What I did was: install liblapack3gf-dev to complete the installations, according to previous suggestions. Now, my guess for the link is LIBS=-L/usr/lib -llapack -L/usr/lib -lstdc++ According to the README, a link to both lapack and lstc++ libraries is needed. No link to the C++ compiler, as the above link is for a plugin for a program that is C++ compiled. Should those LIBS above not be correctly linked, the program complises without the plugin. I am going to try with the above link. If it works, I have to consider whether faster libraries would speed up the plugin. I don't know how heavy the mathematical computations are. I have the MKL libraries, though as rpm package. And since a few years, alien alone is no more capable of transforming that rpm to deb. Probably rpm would install with Debian, though one never knows where the files are. Thanks francesco On Thu, Mar 14, 2013 at 1:19 PM, João Luis Meloni Assirati assir...@nonada.if.usp.br wrote: Em 14-03-2013 08:54, Francesco Pietra escreveu: Please see my previous answer, and action. Directions how to compile that program tell that links to both lapack and lstc++ libraries are required in LIBS=. No link to the C++ compiler is required. Francesco, please answer to the list. I could not see your previous answer nor action. I'm a subscriber of the debian-users list only. João Luis. francesco On Thu, Mar 14, 2013 at 12:21 PM, João Luis Meloni Assirati assir...@nonada.if.usp.br wrote: Em 14-03-2013 08:00, Francesco Pietra escreveu: Hello May I ask how to correctly link lapack and C standard libraries with Debian amd64 wheezy? You mean how to compile a C program, linking both lapack and the standard C library to it? I suppose so in the following. Packages installed: liblapack3gf liblapack3 libblas3 libc6 libc6-dev ** You probably need liblapack-dev also, which contains the header files needed to compile our program. The code to compile makes a generic example: LIBS=-llapack -lstdc++ If it's a C program, you don't need the C++ standard library. Suppose your program is a file program.c. Try gcc -llapack -lm -o program program.c Usually you don't have to explicitly link the standard C library (because it is standard), except the math portions of it (so use the -lm switch if you are using math functions from the standard lib). thanks francesco pietra João Luis. -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmubvzh6g7tj3qwv4e5c42a_tm+qly3mcpnqk1gf9tt...@mail.gmail.com
Fwd: Linking lapack and C standard library
I just came across liblapacke liblapacke-dev for amd64 wheezy. Are these packages what is needed to link lapack header files and so files for a C-language program? If so, can these packages be installed in addition to those already installed: liblapack3gf liblapack3gf-dev thanks francesco pietra -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Thu, Mar 14, 2013 at 6:53 PM Subject: Fwd: Linking lapack and C standard library To: amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org As to the problem of linking lapack, I wonder whether this is because it deal of a C-language code, requiring a fine-tuned calling. Is any C interface to lapack in Debian? thanks francesco -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Thu, Mar 14, 2013 at 6:35 PM Subject: Fwd: Linking lapack and C standard library To: amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org No, it is not correct. With the indicated links, patching reports all correct Hunk(s), while a post script is incorrect. So that make depends for the program+plugin does not correlate anything. I tried the link to -L/usr with same error. It is not clear to me whether it is a problem of path, or of lacking headers. While I see the headers for stdc++ (commanding locate ..., I don't see headers for lapack (having installed liblapack3gf-dev). Perhaps some other lapack package is required. I tried to have a more verbose patching, as the error indicated both on patching and on make depends: plugin.inc:39: *** missing separator. Stop DONE! does not point to a remedy. francesco -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Thu, Mar 14, 2013 at 3:54 PM Subject: Re: Linking lapack and C standard library To: João Luis Meloni Assirati assir...@nonada.if.usp.br, amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org Hello João Luis: Sorry for my lack of care in setting the addresses. What I did was: install liblapack3gf-dev to complete the installations, according to previous suggestions. Now, my guess for the link is LIBS=-L/usr/lib -llapack -L/usr/lib -lstdc++ According to the README, a link to both lapack and lstc++ libraries is needed. No link to the C++ compiler, as the above link is for a plugin for a program that is C++ compiled. Should those LIBS above not be correctly linked, the program complises without the plugin. I am going to try with the above link. If it works, I have to consider whether faster libraries would speed up the plugin. I don't know how heavy the mathematical computations are. I have the MKL libraries, though as rpm package. And since a few years, alien alone is no more capable of transforming that rpm to deb. Probably rpm would install with Debian, though one never knows where the files are. Thanks francesco On Thu, Mar 14, 2013 at 1:19 PM, João Luis Meloni Assirati assir...@nonada.if.usp.br wrote: Em 14-03-2013 08:54, Francesco Pietra escreveu: Please see my previous answer, and action. Directions how to compile that program tell that links to both lapack and lstc++ libraries are required in LIBS=. No link to the C++ compiler is required. Francesco, please answer to the list. I could not see your previous answer nor action. I'm a subscriber of the debian-users list only. João Luis. francesco On Thu, Mar 14, 2013 at 12:21 PM, João Luis Meloni Assirati assir...@nonada.if.usp.br wrote: Em 14-03-2013 08:00, Francesco Pietra escreveu: Hello May I ask how to correctly link lapack and C standard libraries with Debian amd64 wheezy? You mean how to compile a C program, linking both lapack and the standard C library to it? I suppose so in the following. Packages installed: liblapack3gf liblapack3 libblas3 libc6 libc6-dev ** You probably need liblapack-dev also, which contains the header files needed to compile our program. The code to compile makes a generic example: LIBS=-llapack -lstdc++ If it's a C program, you don't need the C++ standard library. Suppose your program is a file program.c. Try gcc -llapack -lm -o program program.c Usually you don't have to explicitly link the standard C library (because it is standard), except the math portions of it (so use the -lm switch if you are using math functions from the standard lib). thanks francesco pietra João Luis. -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmvYtZnNUo+ZD4Mac7dAWgM1hJBBeWFuDaHG6KhEg=w...@mail.gmail.com
Re: RAID1 all bootable
On Wed, Mar 6, 2013 at 8:38 AM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: Bob Proulx wrote: Francesco Pietra wrote: Thanks so much for this manual. Unfortunately, I have no more the initial situation (one HD replaced) because I was hurried by an editor to provide computational data from my CUDA server. I did not want to run the server before all my data were backed up. Therefore I did a fresh amd64 wheezy install on both disks, the old one and the newly replaced. The installation ended with: Sad to see that you have given up already and destroyed your data. I had all my data on another raid1 machine. Following the new install, all data were scp transferred. All my machine are on a router, with passwordless scp. Which is also used to contact external server for computational work. Oh! Okay. I thought you had installed over it. I see now that you installed upon a different system and copied over to it. Very good. Following a seemingly correct installation, with grub installed 'grub-install /dev/sda' and 'update grub' command grub-install /dev/sdb led to a system that did no more boot. I can't see what was wrong with the installation. I have now the same situation (install from the wheezy installer). If you suggest what to check, I'll do that. I can't think of any reason for that to fail. It works for me. (I do always set up a separate /boot but a /boot that is also on RAID1. But it eliminates the LVM interaction. Which previously was not supported but now as I understand it is fully supported.) I am sorry but I cannot think of anything to suggest. I always found grub 1 easier to debug than grub 2. With grub 1 it was possible to do something like this: Verify that the grub files are on both disks: grubfind /grub/stage1 (hd0,0) (hd1,0) Install grub onto the second disk: grub device (hd0) /dev/sdb grub root (hd0,0) grub setup (hd0) grub quit But now with grub 2 there is only the install script: grub-install /dev/sdb I can only suggest that if you have the resources set up a victim machine and do test installations and then try different combinations in order to learn enough about the problem in order to debug it. I had the same idea, though, at the moment, there is no such victim machine, and duties are pressing: classes, research, shortage of money (I am based in Italy, you know the situation from the media). I'll explore with Knoppix. Through Knoppix, in the past, I was able to look into my md0 (boot) and md1 (LVM). I could mount sda and look into it, detecting grub (don't remember which version). However, I did not try to install grub from Knoppix, although it should be feasible. Have a nice day francesco pietra Thanks a lot for your generous help. I (we) learned a lot from you. Happy to help. I only wish it could have been more useful. Bob -- To UNSUBSCRIBE, email to debian-amd64-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130306073823.ga30...@hysteria.proulx.com -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmuGw8z8DT0-NesiWtT=OZK9Q_TzMf=o48p5mv_iun+...@mail.gmail.com
Re: RAID1 all bootable
1.6G 1% /run/shm /dev/md0 176M 19M 148M 11% /boot /dev/mapper/vg1-home 395G 284G 91G 76% /home /dev/mapper/vg1-opt 9.2G 1.5G 7.3G 17% /opt /dev/mapper/vg1-tmp 2.8G 69M 2.6G 3% /tmp /dev/mapper/vg1-usr28G 4.3G 22G 17% /usr /dev/mapper/vg1-var 9.2G 840M 7.9G 10% /var francesco@.:~$ This is the currest status. grub-install /dev/sdb was run with that situation (deriving from install with amd64 wheezy B$ installer downloaded on Feb 1, 2013. That installation ended with grub-install /dev/sda update grub Thanks francesco pietra On Wed, Mar 6, 2013 at 7:02 PM, Shane Johnson s...@rasmussenequipment.com wrote: snip As far as I can remember, I already posted for this system root@.:/home/francesco# cat /proc/mdstat Personalities : [raid1] md1 : active raid1 sda2[0] sdb2[1] 487759680 blocks super 1.2 [2/2] [UU] md0 : active raid1 sda1[0] sdb1[1] 191296 blocks super 1.2 [2/2] [UU] unused devices: none root@.:/home/francesco# francesco@.:~$ df -h FilesystemSize Used Avail Use% Mounted on rootfs938M 185M 705M 21% / udev 10M 0 10M 0% /dev tmpfs 807M 628K 807M 1% /run /dev/mapper/vg1-root 938M 185M 705M 21% / tmpfs 5.0M 0 5.0M 0% /run/lock tmpfs 1.6G 84K 1.6G 1% /run/shm /dev/md0 176M 19M 148M 11% /boot /dev/mapper/vg1-home 395G 284G 91G 76% /home /dev/mapper/vg1-opt 9.2G 1.5G 7.3G 17% /opt /dev/mapper/vg1-tmp 2.8G 69M 2.6G 3% /tmp /dev/mapper/vg1-usr28G 4.3G 22G 17% /usr /dev/mapper/vg1-var 9.2G 840M 7.9G 10% /var francesco@.:~$ the deadly command' grub-install /dev/sdb was run with the system started as above. Thanks francesco pietra snip Francesco, The df -h shows us what is mounted but not if the drives are partitioned or not. Can you do fdisk -l and send us the output of that? Also, you replied directly to me without the mailing list. I have included it in the CC so that everyone can share in the knowledge. Please make sure you always reply to the list.(Reply-all works real good for this.) Thanks -- Shane D. Johnson IT Administrator Rasmussen Equipment -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmtN2SUyvTKqSTAFao14=a1aqwfzeyh7g80-_odstxo...@mail.gmail.com
Re: RAID1 all bootable
On Wed, Mar 6, 2013 at 9:03 PM, Lennart Sorensen lsore...@csclub.uwaterloo.ca wrote: On Wed, Mar 06, 2013 at 08:03:12PM +0100, Francesco Pietra wrote: Sorry, I forgot both the list and the appropriate output; root@:/home/francesco# fdisk -l Disk /dev/sda: 500.1 GB, 500107862016 bytes 255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x000f1911 Device Boot Start End Blocks Id System /dev/sda1 *2048 385023 191488 fd Linux raid autodetect /dev/sda2 385024 976166911 487890944 fd Linux raid autodetect Disk /dev/sdb: 500.1 GB, 500107862016 bytes 255 heads, 63 sectors/track, 60801 cylinders, total 976773168 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0xcca6 Device Boot Start End Blocks Id System /dev/sdb1 *2048 385023 191488 fd Linux raid autodetect /dev/sdb2 385024 976166911 487890944 fd Linux raid autodetect OK, so that is the normal setup with partitions. grub-install /dev/sda and /dev/sdb should have worked fine (but of course it has to be run from the system, not some other thing like knoppix or the like) or from a chroot into the system even if booted from something else. Disk /dev/md0: 195 MB, 195887104 bytes 2 heads, 4 sectors/track, 47824 cylinders, total 382592 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/md0 doesn't contain a valid partition table Disk /dev/md1: 499.5 GB, 499465912320 bytes 2 heads, 4 sectors/track, 121939920 cylinders, total 975519360 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/md1 doesn't contain a valid partition table Disk /dev/mapper/vg1-root: 998 MB, 998244352 bytes 255 heads, 63 sectors/track, 121 cylinders, total 1949696 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/mapper/vg1-root doesn't contain a valid partition table Disk /dev/mapper/vg1-swap: 15.0 GB, 14998831104 bytes 255 heads, 63 sectors/track, 1823 cylinders, total 29294592 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/mapper/vg1-swap doesn't contain a valid partition table Disk /dev/mapper/vg1-usr: 30.0 GB, 29997662208 bytes 255 heads, 63 sectors/track, 3647 cylinders, total 58589184 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/mapper/vg1-usr doesn't contain a valid partition table Disk /dev/mapper/vg1-opt: MB, 220736 bytes 255 heads, 63 sectors/track, 1215 cylinders, total 19529728 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/mapper/vg1-opt doesn't contain a valid partition table Disk /dev/mapper/vg1-var: MB, 220736 bytes 255 heads, 63 sectors/track, 1215 cylinders, total 19529728 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/mapper/vg1-var doesn't contain a valid partition table Disk /dev/mapper/vg1-tmp: 2998 MB, 2998927360 bytes 255 heads, 63 sectors/track, 364 cylinders, total 5857280 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/mapper/vg1-tmp doesn't contain a valid partition table Disk /dev/mapper/vg1-home: 430.0 GB, 43046080 bytes 255 heads, 63 sectors/track, 52277 cylinders, total 839843840 sectors Units = sectors of 1 * 512 = 512 bytes Sector size (logical/physical): 512 bytes / 4096 bytes I/O size (minimum/optimal): 4096 bytes / 4096 bytes Disk identifier: 0x Disk /dev/mapper/vg1-home doesn't contain a valid partition table root@:/home/francesco# root@.:/home/francesco# cat /proc/mdstat Personalities : [raid1] md1 : active raid1 sda2[0] sdb2[1] 487759680
Re: RAID1 all bootable
On Tue, Mar 5, 2013 at 7:30 PM, Bob Proulx b...@proulx.com wrote: Francesco Pietra wrote: Thanks so much for this manual. Unfortunately, I have no more the initial situation (one HD replaced) because I was hurried by an editor to provide computational data from my CUDA server. I did not want to run the server before all my data were backed up. Therefore I did a fresh amd64 wheezy install on both disks, the old one and the newly replaced. The installation ended with: Sad to see that you have given up already and destroyed your data. I had all my data on another raid1 machine. Following the new install, all data were scp transferred. All my machine are on a router, with passwordless scp. Which is also used to contact external server for computational work. Oh well. Nonetheless, I'll try to digest your manual. At this point, could you also describe how to safely proceed, on this situation, to have grub on both disks? It would be useful community wide, to complete the raid1 installation from the Debian installer. As was already mentioned: # grub-install /dev/sda # grub-install /dev/sdb Newer Debian installers will give the option to install to both disks but older ones do not. (on the above situation I commanded grub-install /dev/sdb, whereby, at next boot, grub was no more found, and the system entered grub rescue, from where I restored the situation of grub on sda only. Running 'grub-install /dev/sdb' should work. If it does not then something is wrong. Unfortunately you will need to debug it. Following a seemingly correct installation, with grub installed 'grub-install /dev/sda' and 'update grub' command grub-install /dev/sdb led to a system that did no more boot. I can't see what was wrong with the installation. I have now the same situation (install from the wheezy installer). If you suggest what to check, I'll do that. Thanks a lot for your generous help. I (we) learned a lot from you. francesco pietra Bob -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmtUsckE5fYJpTY-fnkYhZZCH44h4w9J_G=2eqe=0dn...@mail.gmail.com
Re: RAID1 all bootable
Hi Bob: Thanks so much for this manual. Unfortunately, I have no more the initial situation (one HD replaced) because I was hurried by an editor to provide computational data from my CUDA server. I did not want to run the server before all my data were backed up. Therefore I did a fresh amd64 wheezy install on both disks, the old one and the newly replaced. The installation ended with: grub-install /dev/sda update grub Now the situation is (and the same on the server, which has only much larger HDs, and a different balance for opt for the compiled computational codes, non-deb): francesco@..:~$ df -h FilesystemSize Used Avail Use% Mounted on rootfs938M 170M 720M 20% / udev 10M 0 10M 0% /dev tmpfs 807M 628K 807M 1% /run /dev/mapper/vg1-root 938M 170M 720M 20% / tmpfs 5.0M 0 5.0M 0% /run/lock tmpfs 1.6G 148K 1.6G 1% /run/shm /dev/md0 176M 19M 148M 11% /boot /dev/mapper/vg1-home 395G 283G 92G 76% /home /dev/mapper/vg1-opt 9.2G 1.1G 7.7G 13% /opt /dev/mapper/vg1-tmp 2.8G 69M 2.6G 3% /tmp /dev/mapper/vg1-usr28G 3.3G 23G 13% /usr /dev/mapper/vg1-var 9.2G 468M 8.3G 6% /var Nonetheless, I'll try to digest your manual. At this point, could you also describe how to safely proceed, on this situation, to have grub on both disks? It would be useful community wide, to complete the raid1 installation from the Debian installer. (on the above situation I commanded grub-install /dev/sdb, whereby, at next boot, grub was no more found, and the system entered grub rescue, from where I restored the situation of grub on sda only. Thanks and kind regards francesco On Sun, Mar 3, 2013 at 10:26 PM, Bob Proulx b...@proulx.com wrote: Hi Francesco, As far as I can determine reading this thread you have had a RAID1 with two disks sda and sdb. The disk sda failed. But grub was only installed on the failed sda. The disk sdb contains a mirror of everything but does not boot. Earlier in the thread Lennart gave an excellent suggestion: Lennart Sorensen wrote: You can boot the install disk in rescue mode, select the root partition to chroot into, then run grub-install from there. When grub asks where to install, you should configure it for both sda and sdb. I think 'dpkg-reconfigure grub-pc' is where that is selected. Might need it to use -plow to asks all levels of questions. Not sure. +1 for this suggestion. This is definitely the way to go to fix your problem. Francesco Pietra wrote: In my case, with the sda that contained grub loader replaced by a new disk, the rescue mode (using the same CD installer for amd64 wheezy) did not find any partition. Inverting the SATA cables, same result. No partitions at all? That is scary. And I find it to be hard to believe. No partitions would mean that the data from your disks were zeroed out. Perhaps you were mistaken? Please try it again. In both cases (I mean position of SATA cables) I went to the shell in the installer environment: Don't work from the installer environment. Work from the target environment. That is a critical difference! #fisk /dev/sda (or sdb) fisk? That command does not exist in the installer environment. You must have been elsewhere. device contains neither a valid DOS partition table, nor Sun, etc (expected for a raid) Try 'cat /proc/partitions' for a simple safe read-only start. #dmesg |grep -i sd sda (and sbb): unknown partition table (expected for a raid), however md: raid0 md: raid1 were identified, along with rai4, 5, 6 etc (unfortunately | less does not work to see the whole message). Am I using the Rescue Mode improperly? I was unable to dig into the HD that contains md0 (booth loader, EXT2) and md1 ( LVM partitions home tmp usr opt var swap EXT3) I believe you are using rescue mode improperly. I have written about how to use rescue mode several times recently. Here is one posting: http://lists.debian.org/debian-user/2013/01/msg00218.html Here is the official documentation for it: http://www.debian.org/releases/stable/i386/ch08s07.html.en But that is fairly terse. Let me say that the rescue mode looks just like the install mode initially. It will ask you keyboard and locale questions and you might wonder if you are rescuing or installing! But it will have Rescue in the upper left corner so that you can tell that you are not in install mode and be assured. Get the tool set up with keyboard, locale, timezone, and similar and eventually it will give you a menu with a list of actions. Here is a quick run-through. Advanced options... Rescue mode keyboard dialog ...starts networking... hostname dialog domainname dialog ...apt update release files... ...loading additional components, Retrieving udebs... ...detecting disks... Then eventually it will get to a menu
Re: RAID1 all bootable
Is this recipe devised for installing grub on both sda and sda with an undamaged RAID1? In my case, with the sda that contained grub loader replaced by a new disk, the rescue mode (using the same CD installer for amd64 wheezy) did not find any partition. Inverting the SATA cables, same result. In both cases (I mean position of SATA cables) I went to the shell in the installer environment: #fisk /dev/sda (or sdb) device contains neither a valid DOS partition table, nor Sun, etc (expected for a raid) #dmesg |grep -i sd sda (and sbb): unknown partition table (expected for a raid), however md: raid0 md: raid1 were identified, along with rai4, 5, 6 etc (unfortunately | less does not work to see the whole message). Am I using the Rescue Mode improperly? I was unable to dig into the HD that contains md0 (booth loader, EXT2) and md1 ( LVM partitions home tmp usr opt var swap EXT3) Thanks a lot for your kind advice francesco pietra On Fri, Mar 1, 2013 at 10:35 PM, Lennart Sorensen lsore...@csclub.uwaterloo.ca wrote: On Fri, Mar 01, 2013 at 08:20:09PM +0100, Francesco Pietra wrote: Hi: With a raid1 amd64 wheezy, one of the two HDs got broken. Unfortunately, I had added grub to sda only, which is just the one broken. So that, when it is replaced with a fresh HD, the OS is not found. Inverting the SATA cables of course does not help (Operative System Not Found). In a previous similar circumstance, I was lucky that the broken HD was the one without gru. Is any way to recover? perhaps through Knoppix? I know how to look into undamaged RAID1 with Knoppix. Also, when making a fresh RAID1 from scratch, where to find a Debian description of how to make both sda and sdb bootable? (which should be included by default, in my opinion) You can boot the install disk in rescue mode, select the root partition to chroot into, then run grub-install from there. When grub asks where to install, you should configure it for both sda and sdb. I think 'dpkg-reconfigure grub-pc' is where that is selected. Might need it to use -plow to asks all levels of questions. Not sure. -- Len Sorensen -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmvc0+e47n6savowsrctzxdn-7ypg0wn9j1cqukcz1l...@mail.gmail.com
Fwd: RAID1 all bootable
A further piece on information. With knoppix 7.0, the procedure for examining mdadm arrives at cat /proc/partitions sda sdb RAID1 (md0 md1) is not seen. I assume that this is the way Knoppix behaves in this situation. Thanks francesco pietra -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Sat, Mar 2, 2013 at 10:11 AM Subject: Re: RAID1 all bootable To: Lennart Sorensen lsore...@csclub.uwaterloo.ca, amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org Is this recipe devised for installing grub on both sda and sda with an undamaged RAID1? In my case, with the sda that contained grub loader replaced by a new disk, the rescue mode (using the same CD installer for amd64 wheezy) did not find any partition. Inverting the SATA cables, same result. In both cases (I mean position of SATA cables) I went to the shell in the installer environment: #fisk /dev/sda (or sdb) device contains neither a valid DOS partition table, nor Sun, etc (expected for a raid) #dmesg |grep -i sd sda (and sbb): unknown partition table (expected for a raid), however md: raid0 md: raid1 were identified, along with rai4, 5, 6 etc (unfortunately | less does not work to see the whole message). Am I using the Rescue Mode improperly? I was unable to dig into the HD that contains md0 (booth loader, EXT2) and md1 ( LVM partitions home tmp usr opt var swap EXT3) Thanks a lot for your kind advice francesco pietra On Fri, Mar 1, 2013 at 10:35 PM, Lennart Sorensen lsore...@csclub.uwaterloo.ca wrote: On Fri, Mar 01, 2013 at 08:20:09PM +0100, Francesco Pietra wrote: Hi: With a raid1 amd64 wheezy, one of the two HDs got broken. Unfortunately, I had added grub to sda only, which is just the one broken. So that, when it is replaced with a fresh HD, the OS is not found. Inverting the SATA cables of course does not help (Operative System Not Found). In a previous similar circumstance, I was lucky that the broken HD was the one without gru. Is any way to recover? perhaps through Knoppix? I know how to look into undamaged RAID1 with Knoppix. Also, when making a fresh RAID1 from scratch, where to find a Debian description of how to make both sda and sdb bootable? (which should be included by default, in my opinion) You can boot the install disk in rescue mode, select the root partition to chroot into, then run grub-install from there. When grub asks where to install, you should configure it for both sda and sdb. I think 'dpkg-reconfigure grub-pc' is where that is selected. Might need it to use -plow to asks all levels of questions. Not sure. -- Len Sorensen -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmtmhadi2e_uk+wf+c0k9d1ygn3tv91jsr4g2ppp5_a...@mail.gmail.com
Re: RAID1 all bootable
Hi Lennart, Hi Simon A proper understanding of mdadm is required. Hurrying with focus on codes for biochemical applications has brought me into a mess. Relying of all my data, and special compiled programs, present on another raid1 amd64 wheezy, I carried out a reinstall of amd64 wheezy on the machine with new HD. mdo (boot, ext20, md1 (LVM, home, usr, etc). GRUB was installed on /dev/sda Then the command grub-install /dev/sdb with reported installation compete. No errors reported. On rebooting, GRUB was no more found, entering in grub rescue which should also be known accurately, because prefix/root/ are now wrong. The only care I exerted, was not to work with the machine where I have my data, until the damaged machine is in order again. At any event, how to install safely GRUB on both disks of a RAID1 is a must. Thanks for your kind advice. francesco pietra As to mdadm, On Sat, Mar 2, 2013 at 7:05 AM, Simon Vos simon...@gmail.com wrote: Have you assembled you raid devices again (mdadm --assemble /dev/mdX /dev/sdX)? That should still work with the disk that was used for your RAID-1, when that's done you can mount your disk, chroot into it and run grub-install /dev/sda (and grub-install /dev/sdb, so you won't have this problem in the future ;-)). On 2 March 2013 11:10, Francesco Pietra chiendar...@gmail.com wrote: A further piece on information. With knoppix 7.0, the procedure for examining mdadm arrives at cat /proc/partitions sda sdb RAID1 (md0 md1) is not seen. I assume that this is the way Knoppix behaves in this situation. Thanks francesco pietra -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Sat, Mar 2, 2013 at 10:11 AM Subject: Re: RAID1 all bootable To: Lennart Sorensen lsore...@csclub.uwaterloo.ca, amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org Is this recipe devised for installing grub on both sda and sda with an undamaged RAID1? In my case, with the sda that contained grub loader replaced by a new disk, the rescue mode (using the same CD installer for amd64 wheezy) did not find any partition. Inverting the SATA cables, same result. In both cases (I mean position of SATA cables) I went to the shell in the installer environment: #fisk /dev/sda (or sdb) device contains neither a valid DOS partition table, nor Sun, etc (expected for a raid) #dmesg |grep -i sd sda (and sbb): unknown partition table (expected for a raid), however md: raid0 md: raid1 were identified, along with rai4, 5, 6 etc (unfortunately | less does not work to see the whole message). Am I using the Rescue Mode improperly? I was unable to dig into the HD that contains md0 (booth loader, EXT2) and md1 ( LVM partitions home tmp usr opt var swap EXT3) Thanks a lot for your kind advice francesco pietra On Fri, Mar 1, 2013 at 10:35 PM, Lennart Sorensen lsore...@csclub.uwaterloo.ca wrote: On Fri, Mar 01, 2013 at 08:20:09PM +0100, Francesco Pietra wrote: Hi: With a raid1 amd64 wheezy, one of the two HDs got broken. Unfortunately, I had added grub to sda only, which is just the one broken. So that, when it is replaced with a fresh HD, the OS is not found. Inverting the SATA cables of course does not help (Operative System Not Found). In a previous similar circumstance, I was lucky that the broken HD was the one without gru. Is any way to recover? perhaps through Knoppix? I know how to look into undamaged RAID1 with Knoppix. Also, when making a fresh RAID1 from scratch, where to find a Debian description of how to make both sda and sdb bootable? (which should be included by default, in my opinion) You can boot the install disk in rescue mode, select the root partition to chroot into, then run grub-install from there. When grub asks where to install, you should configure it for both sda and sdb. I think 'dpkg-reconfigure grub-pc' is where that is selected. Might need it to use -plow to asks all levels of questions. Not sure. -- Len Sorensen -- To UNSUBSCRIBE, email to debian-amd64-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmtmhadi2e_uk+wf+c0k9d1ygn3tv91jsr4g2ppp5_a...@mail.gmail.com -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmtuc4i2swgdq_bgge+-_uks7ywxveg2xmynyoynjxi...@mail.gmail.com
RAID1 all bootable
Hi: With a raid1 amd64 wheezy, one of the two HDs got broken. Unfortunately, I had added grub to sda only, which is just the one broken. So that, when it is replaced with a fresh HD, the OS is not found. Inverting the SATA cables of course does not help (Operative System Not Found). In a previous similar circumstance, I was lucky that the broken HD was the one without gru. Is any way to recover? perhaps through Knoppix? I know how to look into undamaged RAID1 with Knoppix. Also, when making a fresh RAID1 from scratch, where to find a Debian description of how to make both sda and sdb bootable? (which should be included by default, in my opinion) Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmu_dekcz7fx9fydnpuoaa9j3kkc+7zfkvf-ss7b7p6...@mail.gmail.com
Running 32bit OpenGL program with amd64
Hello: I would like to continue to use a 32bit graphical program based on OpenGL. It worked well on i386, requiring libXm.so.3 (from libmotif3). Is it conceivable to simply add libXm.so.3 (taken from my dismissed i388 PC) to ia32-libs? Thanks for advice francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmvNMH5hH_=p3mrlpa6uhth+n_zwhkv3eg3bxxo9p1-...@mail.gmail.com
Re: gnome-session charsh
I am bound to gnome for the program gchempaint. In my experience, it is the only program, freely available as gnu, that allows drawing chemical structures as required by chemical journals. jchempaint is based on gtk, therefore, in principle, it might run on other window managers based on gtk. However, if not offered as precompiled (as within gnome), it is extremely arduous to compile. Otherwise, I am unhappy with gnome, not only for what I wrote, but also because it lacks decent burners and pdf tools (I installed k3b and okular from kde, to this purpose). One should also take into account that VMD, used universally as 3D viewer in combination with molecular dynamics and other science, looks for GPU cards, to accelerate very heavy processes. I never tried if a simple window manager provides adequate support to that. What I blame of GNOME is that it wants to take possession of the computer. startxx / gnome-session avoids this, but presently it requires (perhaps) some extra settings, in order to avoid crashes. KDE is even worse to this respect. Finally, with so much automatic steps with gnome/kde, knowledge of unix is being lost, people converge to microsoft/apple the more and more. francesco On Sat, Aug 25, 2012 at 7:25 AM, Chris Bannister cbannis...@slingshot.co.nz wrote: On Fri, Aug 24, 2012 at 03:34:35PM +0200, Francesco Pietra wrote: I suggest that in Debian mirrors, gnome is so arranged that launching it be an optional. In computational chemistry/biochemistry, particularly with amd64, most work is at the linux prompt. Now, with It would be better not to install gnome at all then. Just install a basic window manager, and open an xterm as needed. -- If you're not careful, the newspapers will have you hating the people who are being oppressed, and loving the people who are doing the oppressing. --- Malcolm X -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmsk4nw2nce7hi9vtqt4wjumpsab+65tqmr1fm5zocz...@mail.gmail.com
gnome-session charsh
Hi all: Since the latest gnome, the sequence startx gnome-session is often attended by hanging of linux at gnome-session with both i386 and amd64 wheezy. Gnome dislikes much more than in the past not be set completely free. I suggest that in Debian mirrors, gnome is so arranged that launching it be an optional. In computational chemistry/biochemistry, particularly with amd64, most work is at the linux prompt. Now, with the advent of CPU-GPU systems, the graphic interface is used with servers ans testing version, too. But only at certain stages. Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmuV=wrwi-yzl_urxmedsuo3zo9wfqq9ohcxkjo4x7c...@mail.gmail.com
package wxmacmolplt broken
Hi all: Package wxmacmolplt on wheezy is broken. It currently requires libglew1.6, while libglew1.7 is currently installed. thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmvkuqgnerdgukbavt0qvvow9ieasvvkeyzmzabtakt...@mail.gmail.com
i386 testing: java not recognizing its libraries and libreoffice not launching
Following update/upgrade, java does not recognize libjli.so any more. I had to set LD_LIBRARY... to remedy. Nonetheless, libreoffice does not start any more: francesco@deb32:~$ libreoffice terminate called after throwing an instance of 'com::sun::star::uno::RuntimeException' francesco@deb32:~$ I thought it is a java problem. What else? Incidentally, I turned to AbiWORD for my .dot table. Unless my i386 testing has major problems, that text editor is simply unusable for complex tables. In general, while at the linux prompt Debian works well (in particular amd64 testing, here in use for a GPU-CPU cluster), once gnome is launched installed, problems arise. Too many things that in science are not used, too much done automatically, and often erroneously. I am at gnome simply for gchempaint, other wise there is no decent pdf reader not CD burner, which are useful to any purpose. I had to install okular and k3b, making the complex even more complex. With such stuff as gnome, which even pretends to take care of upgrading, newcomers will not even learn how to mount a device. Thanks for advice about libreoffice francesco pietra PS: I am not at the stable i386 version simply to have a correspondence with testing amd64 which we have to use for recent nvidia drivers for GPU-CPU clusters. -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmvQsv-FSG90By0=ohg4vx7mlzpwmjp-ktgue9rtyex...@mail.gmail.com
Fwd: i386 testing: java not recognizing its libraries and libreoffice and okular not launching
In addition, I have now noticed that even okular does not start anymore after that infamous apt-get update/upgrade with i386 testing: francesco@deb32:~$ okular okular(3765): you need to call Settings::instance before using KCrash: Application 'okular' crashing... KCrash: Attempting to start /usr/lib/kde4/libexec/drkonqi from kdeinit sock_file=/home/francesco/.kde/socket-deb32/kdeinit4__0 Warning: connect() failed: : No such file or directory KCrash: Attempting to start /usr/lib/kde4/libexec/drkonqi directly drkonqi(3766): Unable to find an internal debugger that can work with the KCrash backend [1]+ Stopped okular francesco@deb32:~$ -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Mon, Jul 2, 2012 at 3:52 PM Subject: i386 testing: java not recognizing its libraries and libreoffice not launching To: debian-users debian-user@lists.debian.org Following update/upgrade, java does not recognize libjli.so any more. I had to set LD_LIBRARY... to remedy. Nonetheless, libreoffice does not start any more: francesco@deb32:~$ libreoffice terminate called after throwing an instance of 'com::sun::star::uno::RuntimeException' francesco@deb32:~$ I thought it is a java problem. What else? Incidentally, I turned to AbiWORD for my .dot table. Unless my i386 testing has major problems, that text editor is simply unusable for complex tables. In general, while at the linux prompt Debian works well (in particular amd64 testing, here in use for a GPU-CPU cluster), once gnome is launched installed, problems arise. Too many things that in science are not used, too much done automatically, and often erroneously. I am at gnome simply for gchempaint, other wise there is no decent pdf reader not CD burner, which are useful to any purpose. I had to install okular and k3b, making the complex even more complex. With such stuff as gnome, which even pretends to take care of upgrading, newcomers will not even learn how to mount a device. Thanks for advice about libreoffice francesco pietra PS: I am not at the stable i386 version simply to have a correspondence with testing amd64 which we have to use for recent nvidia drivers for GPU-CPU clusters. -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmvaddngi9wmvevqlqzqouwh+vm2ecan2d9mbt+v7kb...@mail.gmail.com
why ABIWORD?
Hello: With my i386 wheezy, a today update/upgrade led to libreoffice (text) not launching. I resorted to abiword, new in my experience. I found abiword in great troubles with tables made by libreoffice odt. Suddendly, abiword was able to destroy nearly completely the content of the big table. Should my experience be representative, it would be better not to propose text editors that are unable to do what they should. Cheers francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nms-me1ffg1vs0ynj_28ic2zgqcynuc32kgvqyxwfmq...@mail.gmail.com
iceaweasel experimental is not true firefox in my hands
The message below was intended to pkg-mozilla-maintain...@lists.alioth.debian.org list google mail complains that such address does not exist Hi I have followed all your instructions in upgrading iceaweasel to iceweasel beta on i386 wheezy. All went on as described at http://mozilla.debian.net/; without any error message. However, google still complains that the installed browser is inadequate. It is, in fact, probably because I am missing something: ---Google mail is not treated as it should, i.e., there is no key to delete all trashed mail in a single step, for example. This requires the extra work of labeling all messages, one by one, to delete them. Also, although I installed version 7, java does not work with the web. Separately I have mozilla firefox'. launching it, google mail does not complain and the above said key exists. Thanks for your kind attention Francesco Pietra Professor of Chemistry Accademia Lucchese di Scienze, Lettere e Arti, founded in 1584 Palazzo Ducale I-55100 Lucca tel/fax +39 0583 417336 -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmuvz-=m--pNiHOmyR0Xua+hL=whb+vcatv3-z+wyz9...@mail.gmail.com
Having Mozilla Firefox as default web browser
Hi Following extensive upgrading of 1386 wheezy, I am unable to get easily Mozilla Firefox as web browser. I have to commad with full path to its installation. Iceweasel is unable to treat Google Mail adequately. More importantly, Iceaweasel is unable to talk in/back with my connections to certain scientific software. How to eliminate all web browser to leave Mozilla Firefox? thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmskwsw8b2_++uwz4yzc+4gaeh7any5que4tmn+pe0v...@mail.gmail.com
Re: about java and wheezy
Gary Dale garydale at rogers.com writes: On 13/05/12 01:28 PM, Francesco Pietra wrote: Hi Installation of openjdk-6-jdk in wheezy i386 would lead to deletion of much gnome, including openoffice, with reinstallation of gnome and abiword, but not of openoffice/libreoffice, if I understand. Otherwise, java is often useful. Any suggestion about? thanks francesco pietra OpenOffice is usually not in a modern disto like Wheezy. Instead it uses LibreOffice. I have LibreOffice and openjdk working fine in Wheezy with or without Gnome (I normally use KDE but installed Gnome to try it out and to use when KDE gives me problems in Wheezy). If openjdk is replacing a different jdk, it could be that the removal/reinstallation is really updating the jdk setup and links. In answer to all who kindly considered the matter. I was to quick in posting. Having upgraded from squeeze to wheezy i386 I ha such troubles. Then , wanting emacs gchempaint, and pieces of kde (okular k3b), gnome 2 was updated to gnome3, which I did not know. I could install libreoffice, true firefox (avoiding iceweasel which does not support google fully and, more importantly, some of my connections to servers) and openjdk-6-jdk (now without any deletion). However, although firefox is set to java, java does not work in running common molecular applications (movies). Is any independent test of such installation of java available? Which outputs should I show in order to get help? Thanks chiendarret -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/loom.20120514t150557-...@post.gmane.org
about java and wheezy
Hi Installation of openjdk-6-jdk in wheezy i386 would lead to deletion of much gnome, including openoffice, with reinstallation of gnome and abiword, but not of openoffice/libreoffice, if I understand. Otherwise, java is often useful. Any suggestion about? thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmskyrsfpse7hzdm136lm627wggp9fsu4auodta3hk1...@mail.gmail.com
iceweasel no more support by google
Since new google and gnome 3 advent, iceweasel is said not to be supported. I can't access my institutional email address. It is indicated to install either google own web browser or mozilla. Why so and why google does distinguish between iceaweasel and mozilla? With my old desktop an small HD (to spare money for servers) I am having problems of disk space, while most of gnome is not useful to me and gnome 3, installed following uninstall of gnome in wheezy, is giving so many troubles. thanks for advice francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmuaut9th29357ugnx_pq8azmdk3ohtr1rxexsji3hz...@mail.gmail.com
Fwd: installer fails to configure DHCP
-- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Mon, Nov 28, 2011 at 11:46 AM Subject: Re: installer fails to configure DHCP To: Vasileios Karaklioumis plandr...@gmail.com The router works fine with the computer I was referring to and with all other computers. It is the same that in the past let the installers work. fp On Mon, Nov 28, 2011 at 10:31 AM, Vasileios Karaklioumis plandr...@gmail.com wrote: Same happens to me in both archs.I suspect is the routers' fault. On Nov 28, 2011 11:24 AM, Goswin von Brederlow goswin-...@web.de wrote: Francesco Pietra chiendar...@gmail.com writes: Installer debian-testing-i386-netinst.iso downloaded Nov27 2011 fails And why would the AMD64 list be interested in failures of I386? MfG Goswin -- To UNSUBSCRIBE, email to debian-amd64-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/874nxomwfq.fsf@frosties.localnet -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nmsQ_KyJUtREH5k12ogyJq7Ed28o=xb-birsbu3bwjl...@mail.gmail.com
installer fails to configure DHCP
Installer debian-testing-i386-netinst.iso downloaded Nov27 2011 fails to configure DHCP either automatically, with hostname, or manually. Otherwise, the Realtek card works perfectly on this machine (I just wanted to reinstall in order to reshape partitions). Then, I noticed that this is a standing bug: The sole chance I am given for my LVM is to shrink /home to provide space for /usr, whici is short of space. Not an alluring project, as if it fails I am without OS. Debian Bug report logs - #520285 installation-reports: The squeeze netinst dosn't configure DHCP Package: debian-installer; Maintainer for debian-installer is Debian Install System Team debian-b...@lists.debian.org; Source for debian-installer is src:debian-installer. Reported by: Alexander V.Inyakin alexandre.inya...@cern.ch Date: Wed, 18 Mar 2009 16:54:01 UTC francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nms2VVCmAY_3riXgh1R+JreEZxnGgQO6hCZxM=_sy+b...@mail.gmail.com
Preventing gnome3 autosuspend
I would be grateful for instructions how to prevent gnome3 (i386 wheezy) autosuspending. I tried from /usr system wide by either commenting out or false/true, at no avail thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/caev0nmtsogisnbr+_knfn-8esemdqg_q77vkmomkujnsp5t...@mail.gmail.com
nautilus file browser by name
Nautilus file browser uses its concept of ordering files by name. While the gnome2 terminal does that correctly, the file browser mixes up files, which, for computational chemistry, in the presence of many composite names, is not what it should. For example, min-01_02.coor par_ara.inp FE-OXY_colvars.in and many other in between before: min-01_02.conf That should be corrected, or information given which alternative file browser could be used to get the alphabetically correct order (like from the terminal window, where all min* files are grouped together) Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAEv0nms-KDG_SzPJu-0ph86Us5ju9ZB7SSp0J=EvrfVkLb=m...@mail.gmail.com
Fwd: SOLVED PRINTER/FLASHCARD CLOSED THREAD On upgrading to wheezy neither printer nor scanner work anymore.
Solved printer by unistalling printer and all supporting packages and reinstalling hp.. packages. Solved usb_flshcard by either mounting manually or installing 'usb mount' and manually umount. Not clear what was due to fsttab. Scanner: new thread -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Sun, Jun 26, 2011 at 11:10 PM Subject: On upgrading to wheezy neither printer nor scanner work anymore. To: debian-users debian-user@lists.debian.org I have dist upgraded from squeeze to testing (wheezy) 32 bit, getting the linux image and headers 2.6.39-2-686-pae, gnome 2.30.2. Attached HP Scanjet 6200C (scsi), Nikon Coolscan V (usb), and HP deskjet D4260 do not work any more. The latter is said ready but does not print. The queue had to be canceled (cancel#). Both hplip and hpijs are installed. The two scanners were not seen. From /var/log/syslog: ip 08400157 sp bfb1f270 error 4 in vuescan[8048000+648000] Jun 26 14:41:28 deb32 kernel: [ 368.742962] vuescan[2569]: segfault at b2008118 ip 08400157 sp bfdf5a00 error 4 in vuescan[8048000+648000] Jun 26 14:47:20 deb32 kernel: [ 720.536025] usb 6-4: new high speed USB device number 4 using ehci_hcd Jun 26 14:47:20 deb32 kernel: [ 720.670944] usb 6-4: New USB device found, idVendor=04b0, idProduct=4001 Jun 26 14:47:20 deb32 kernel: [ 720.670951] usb 6-4: New USB device strings: Mfr=1, Product=2, SerialNumber=0 Jun 26 14:47:20 deb32 kernel: [ 720.670955] usb 6-4: Product: LS-50 ED Jun 26 14:47:20 deb32 kernel: [ 720.670959] usb 6-4: Manufacturer: Nikon Jun 26 14:47:20 deb32 mtp-probe: checking bus 6, device 4: /sys/devices/pci:00/:00:1e.0/:02:01.2/usb6/6-4 Jun 26 14:47:20 deb32 mtp-probe: bus: 6, device: 4 was not an MTP device Jun 26 14:48:38 deb32 kernel: [ 799.292553] vuescan[2640]: segfault at b2132118 ip 08400157 sp bfab92c0 error 4 in vuescan[8048000+648000] deb32:/var/log# Apart from vuescan, also sane did not find the HP scanner. ls -l /dev/sg* did not identify the HP scanner. Inserting a flashcard into usb expects root permission: Unable to mount Kingston, not authorized. /etc/fstab was automatically touched by the installation: /etc/fstab: francesco@deb32:~$ cat /etc/fstab # /etc/fstab: static file system information. # # file system mount point type options dump pass proc /proc proc defaults 0 0 /dev/mapper/deb32-root / ext3 errors=remount-ro 0 1 # /dev/hda1 /boot ext2 defaults 0 2 UUID=7e0be6ef-6aeb-472b-8f65-4344f46948eb /boot ext2 defaults 0 2 /dev/mapper/deb32-home /home ext3 defaults 0 2 /dev/mapper/deb32-tmp /tmp ext3 defaults 0 2 /dev/mapper/deb32-usr /usr ext3 defaults 0 2 /dev/mapper/deb32-var /var ext3 defaults 0 2 /dev/mapper/deb32-swap_1 none swap sw 0 0 /dev/hdd /media/cdrom0 udf,iso9660 user,noauto 0 0 # /dev/hdc /media/cdrom1 udf,iso9660 user,noauto 0 0 /dev/cdrom3 /media/cdrom1 udf,iso9660 user,noauto 0 0 /dev/fd0 /media/floppy0 auto rw,user,noauto 0 0 # /dev/hdb1 /mnt/hd_slave auto user,rw 0 0 UUID=1db050f6-8895-41d9-9164-77d1aeb170db /mnt/hd_slave auto user,rw but it seems to me to be in order. lsmod: francesco@deb32:~$ lsmod Module Size Used by usb_storage 34951 0 uas 12975 0 mperf 12387 0 speedstep_lib 12463 0 cpufreq_powersave 12422 0 cpufreq_stats 12670 0 cpufreq_conservative 12987 0 cpufreq_userspace 12520 0 ppdev 12621 0 lp 12858 0 fuse 55666 1 nfsd 196206 2 nfs 219235 0 lockd 60891 2 nfsd,nfs fscache 31438 1 nfs auth_rpcgss 31819 2 nfsd,nfs nfs_acl 12463 2 nfsd,nfs sunrpc 137017 6 nfsd,nfs,lockd,auth_rpcgss,nfs_acl ext2 53488 1 loop 1 0 snd_wavefront 30608 0 snd_cs4236 26314 0 snd_intel8x0 22287 0 snd_wss_lib 22401 2 snd_wavefront,snd_cs4236 snd_ac97_codec 83732 1 snd_intel8x0 snd_opl3_lib 13141 2 snd_wavefront,snd_cs4236 ac97_bus 12462 1 snd_ac97_codec snd_hwdep 12906 2 snd_wavefront,snd_opl3_lib snd_pcm_oss 35864 0 snd_mixer_oss 17649 1 snd_pcm_oss snd_pcm 52731 5 snd_cs4236,snd_intel8x0,snd_wss_lib,snd_ac97_codec,snd_pcm_oss snd_mpu401 12592 0 snd_mpu401_uart 13299 3 snd_wavefront,snd_cs4236,snd_mpu401 snd_seq_midi 12744 0 snd_rawmidi 22407 3 snd_wavefront,snd_mpu401_uart,snd_seq_midi snd_seq_midi_event 13124 1 snd_seq_midi snd_seq 39172 2 snd_seq_midi,snd_seq_midi_event snd_timer 22171 4 snd_wss_lib,snd_opl3_lib,snd_pcm,snd_seq usblp 17083 0 snd_seq_device 12995 4 snd_opl3_lib,snd_seq_midi,snd_rawmidi,snd_seq snd 38189 16 snd_wavefront,snd_cs4236,snd_intel8x0,snd_wss_lib,snd_ac97_codec,snd_opl3_lib,snd_hwdep,snd_pcm_oss, snd_mixer_oss,snd_pcm,snd_mpu401,snd_mpu401_uart,snd_rawmidi,snd_seq,snd_timer,snd_seq_device i2c_i801 12670 0 i2c_core 19022 1 i2c_i801 parport_pc 21895 1 evdev 13084 7 psmouse 45863 0 snd_page_alloc 12841 3 snd_intel8x0,snd_wss_lib,snd_pcm rng_core 12550 0 soundcore 12878 1 snd ns558 12417 0 serio_raw 12758 0 shpchp 26653 0 gameport 13332 2 ns558 pcspkr 12515 0 parport 27018 3 ppdev,lp,parport_pc processor 26983 0 button 12783 0 pci_hotplug 26303 1 shpchp ext3 102125 6 jbd 40818 1 ext3 mbcache 12810 2 ext2,ext3 dm_mod 56401 18 sg 21385 0
On upgrading to wheezy neither printer nor scanner work anymore.
,thermal 8139cp 22004 0 mii 12595 3 8139too,8139cp,e100 francesco@deb32:~$ File 'devices' under /proc/bus/usb does not exist. Thanks for advice francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/BANLkTi=itehunfx86gfksfrsbh6kbip...@mail.gmail.com
Fwd: On upgrading to wheezy neither printer nor scanner work anymore.
Perhaps relevant to the problems in this thread: deb32:/home/francesco# hp-plugin HP Linux Imaging and Printing System (ver. 3.11.5) Plugin Download and Install Utility ver. 2.1 Copyright (c) 2001-9 Hewlett-Packard Development Company, LP This software comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to distribute it under certain conditions. See COPYING file for more details. error: PolicyKit support requires DBUS or PolicyKit support files missing ** GLib-GIO:ERROR:/build/buildd-glib2.0_2.28.6-1-i386-A3fp41/glib2.0-2.28.6/./gio/gdbusconnection.c:2279:initable_init: assertion failed: (connection-initialization_error == NULL) Aborted deb32:/home/francesco# -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Sun, Jun 26, 2011 at 11:10 PM Subject: On upgrading to wheezy neither printer nor scanner work anymore. To: debian-users debian-user@lists.debian.org I have dist upgraded from squeeze to testing (wheezy) 32 bit, getting the linux image and headers 2.6.39-2-686-pae, gnome 2.30.2. Attached HP Scanjet 6200C (scsi), Nikon Coolscan V (usb), and HP deskjet D4260 do not work any more. The latter is said ready but does not print. The queue had to be canceled (cancel#). Both hplip and hpijs are installed. The two scanners were not seen. From /var/log/syslog: ip 08400157 sp bfb1f270 error 4 in vuescan[8048000+648000] Jun 26 14:41:28 deb32 kernel: [ 368.742962] vuescan[2569]: segfault at b2008118 ip 08400157 sp bfdf5a00 error 4 in vuescan[8048000+648000] Jun 26 14:47:20 deb32 kernel: [ 720.536025] usb 6-4: new high speed USB device number 4 using ehci_hcd Jun 26 14:47:20 deb32 kernel: [ 720.670944] usb 6-4: New USB device found, idVendor=04b0, idProduct=4001 Jun 26 14:47:20 deb32 kernel: [ 720.670951] usb 6-4: New USB device strings: Mfr=1, Product=2, SerialNumber=0 Jun 26 14:47:20 deb32 kernel: [ 720.670955] usb 6-4: Product: LS-50 ED Jun 26 14:47:20 deb32 kernel: [ 720.670959] usb 6-4: Manufacturer: Nikon Jun 26 14:47:20 deb32 mtp-probe: checking bus 6, device 4: /sys/devices/pci:00/:00:1e.0/:02:01.2/usb6/6-4 Jun 26 14:47:20 deb32 mtp-probe: bus: 6, device: 4 was not an MTP device Jun 26 14:48:38 deb32 kernel: [ 799.292553] vuescan[2640]: segfault at b2132118 ip 08400157 sp bfab92c0 error 4 in vuescan[8048000+648000] deb32:/var/log# Apart from vuescan, also sane did not find the HP scanner. ls -l /dev/sg* did not identify the HP scanner. Inserting a flashcard into usb expects root permission: Unable to mount Kingston, not authorized. /etc/fstab was automatically touched by the installation: /etc/fstab: francesco@deb32:~$ cat /etc/fstab # /etc/fstab: static file system information. # # file system mount point type options dump pass proc /proc proc defaults 0 0 /dev/mapper/deb32-root / ext3 errors=remount-ro 0 1 # /dev/hda1 /boot ext2 defaults 0 2 UUID=7e0be6ef-6aeb-472b-8f65-4344f46948eb /boot ext2 defaults 0 2 /dev/mapper/deb32-home /home ext3 defaults 0 2 /dev/mapper/deb32-tmp /tmp ext3 defaults 0 2 /dev/mapper/deb32-usr /usr ext3 defaults 0 2 /dev/mapper/deb32-var /var ext3 defaults 0 2 /dev/mapper/deb32-swap_1 none swap sw 0 0 /dev/hdd /media/cdrom0 udf,iso9660 user,noauto 0 0 # /dev/hdc /media/cdrom1 udf,iso9660 user,noauto 0 0 /dev/cdrom3 /media/cdrom1 udf,iso9660 user,noauto 0 0 /dev/fd0 /media/floppy0 auto rw,user,noauto 0 0 # /dev/hdb1 /mnt/hd_slave auto user,rw 0 0 UUID=1db050f6-8895-41d9-9164-77d1aeb170db /mnt/hd_slave auto user,rw but it seems to me to be in order. lsmod: francesco@deb32:~$ lsmod Module Size Used by usb_storage 34951 0 uas 12975 0 mperf 12387 0 speedstep_lib 12463 0 cpufreq_powersave 12422 0 cpufreq_stats 12670 0 cpufreq_conservative 12987 0 cpufreq_userspace 12520 0 ppdev 12621 0 lp 12858 0 fuse 55666 1 nfsd 196206 2 nfs 219235 0 lockd 60891 2 nfsd,nfs fscache 31438 1 nfs auth_rpcgss 31819 2 nfsd,nfs nfs_acl 12463 2 nfsd,nfs sunrpc 137017 6 nfsd,nfs,lockd,auth_rpcgss,nfs_acl ext2 53488 1 loop 1 0 snd_wavefront 30608 0 snd_cs4236 26314 0 snd_intel8x0 22287 0 snd_wss_lib 22401 2 snd_wavefront,snd_cs4236 snd_ac97_codec 83732 1 snd_intel8x0 snd_opl3_lib 13141 2 snd_wavefront,snd_cs4236 ac97_bus 12462 1 snd_ac97_codec snd_hwdep 12906 2 snd_wavefront,snd_opl3_lib snd_pcm_oss 35864 0 snd_mixer_oss 17649 1 snd_pcm_oss snd_pcm 52731 5 snd_cs4236,snd_intel8x0,snd_wss_lib,snd_ac97_codec,snd_pcm_oss snd_mpu401 12592 0 snd_mpu401_uart 13299 3 snd_wavefront,snd_cs4236,snd_mpu401 snd_seq_midi 12744 0 snd_rawmidi 22407 3 snd_wavefront,snd_mpu401_uart,snd_seq_midi snd_seq_midi_event 13124 1 snd_seq_midi snd_seq 39172 2 snd_seq_midi,snd_seq_midi_event snd_timer 22171 4 snd_wss_lib,snd_opl3_lib,snd_pcm,snd_seq usblp 17083 0 snd_seq_device 12995 4 snd_opl3_lib,snd_seq_midi,snd_rawmidi,snd_seq snd 38189 16 snd_wavefront,snd_cs4236,snd_intel8x0,snd_wss_lib,snd_ac97_codec,snd_opl3_lib,snd_hwdep,snd_pcm_oss, snd_mixer_oss,snd_pcm,snd_mpu401,snd_mpu401_uart,snd_rawmidi,snd_seq,snd_timer,snd_seq_device
Fwd: On upgrading to wheezy neither printer nor scanner work anymore.
Also relevant what appears on Spanish debian forum: # gedit (gedit:6056): EggSMClient-WARNING **: Failed to connect to the session manager: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed ** GLib-GIO:ERROR:/build/buildd-glib2.0_2.28.6-1-i386-A3fp41/glib2.0-2.28.6/./gio/gdbusconnection.c:2279:initable_init: assertion failed: (connection-initialization_error == NULL) Abortado El problema parece ser el que fué solucionado en http://www.esdebian.org/foro/46879/problemas-driver-intel-gedit De la siguiente forma: # mkdir /usr/lib/i386-linux-gnu/ # ln -s /usr/lib/dri/ /usr/lib/i386-linux-gnu Ahora bien, mi consulta es: si se trata de un bug, conviene aplicar esa solución o es mejor esperar a que se resuelva? Y por otra parte el directorio que se sugiere crear yo ya lo tengo. -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Sun, Jun 26, 2011 at 11:26 PM Subject: Fwd: On upgrading to wheezy neither printer nor scanner work anymore. To: debian-users debian-user@lists.debian.org Perhaps relevant to the problems in this thread: deb32:/home/francesco# hp-plugin HP Linux Imaging and Printing System (ver. 3.11.5) Plugin Download and Install Utility ver. 2.1 Copyright (c) 2001-9 Hewlett-Packard Development Company, LP This software comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to distribute it under certain conditions. See COPYING file for more details. error: PolicyKit support requires DBUS or PolicyKit support files missing ** GLib-GIO:ERROR:/build/buildd-glib2.0_2.28.6-1-i386-A3fp41/glib2.0-2.28.6/./gio/gdbusconnection.c:2279:initable_init: assertion failed: (connection-initialization_error == NULL) Aborted deb32:/home/francesco# -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Sun, Jun 26, 2011 at 11:10 PM Subject: On upgrading to wheezy neither printer nor scanner work anymore. To: debian-users debian-user@lists.debian.org I have dist upgraded from squeeze to testing (wheezy) 32 bit, getting the linux image and headers 2.6.39-2-686-pae, gnome 2.30.2. Attached HP Scanjet 6200C (scsi), Nikon Coolscan V (usb), and HP deskjet D4260 do not work any more. The latter is said ready but does not print. The queue had to be canceled (cancel#). Both hplip and hpijs are installed. The two scanners were not seen. From /var/log/syslog: ip 08400157 sp bfb1f270 error 4 in vuescan[8048000+648000] Jun 26 14:41:28 deb32 kernel: [ 368.742962] vuescan[2569]: segfault at b2008118 ip 08400157 sp bfdf5a00 error 4 in vuescan[8048000+648000] Jun 26 14:47:20 deb32 kernel: [ 720.536025] usb 6-4: new high speed USB device number 4 using ehci_hcd Jun 26 14:47:20 deb32 kernel: [ 720.670944] usb 6-4: New USB device found, idVendor=04b0, idProduct=4001 Jun 26 14:47:20 deb32 kernel: [ 720.670951] usb 6-4: New USB device strings: Mfr=1, Product=2, SerialNumber=0 Jun 26 14:47:20 deb32 kernel: [ 720.670955] usb 6-4: Product: LS-50 ED Jun 26 14:47:20 deb32 kernel: [ 720.670959] usb 6-4: Manufacturer: Nikon Jun 26 14:47:20 deb32 mtp-probe: checking bus 6, device 4: /sys/devices/pci:00/:00:1e.0/:02:01.2/usb6/6-4 Jun 26 14:47:20 deb32 mtp-probe: bus: 6, device: 4 was not an MTP device Jun 26 14:48:38 deb32 kernel: [ 799.292553] vuescan[2640]: segfault at b2132118 ip 08400157 sp bfab92c0 error 4 in vuescan[8048000+648000] deb32:/var/log# Apart from vuescan, also sane did not find the HP scanner. ls -l /dev/sg* did not identify the HP scanner. Inserting a flashcard into usb expects root permission: Unable to mount Kingston, not authorized. /etc/fstab was automatically touched by the installation: /etc/fstab: francesco@deb32:~$ cat /etc/fstab # /etc/fstab: static file system information. # # file system mount point type options dump pass proc /proc proc defaults 0 0 /dev/mapper/deb32-root / ext3 errors=remount-ro 0 1 # /dev/hda1 /boot ext2 defaults 0 2 UUID=7e0be6ef-6aeb-472b-8f65-4344f46948eb /boot ext2 defaults 0 2 /dev/mapper/deb32-home /home ext3 defaults 0 2 /dev/mapper/deb32-tmp /tmp ext3 defaults 0 2 /dev/mapper/deb32-usr /usr ext3 defaults 0 2 /dev/mapper/deb32-var /var ext3 defaults 0 2 /dev/mapper/deb32-swap_1 none swap sw 0 0 /dev/hdd /media/cdrom0 udf,iso9660 user,noauto 0 0 # /dev/hdc /media/cdrom1 udf,iso9660 user,noauto 0 0 /dev/cdrom3 /media/cdrom1 udf,iso9660 user,noauto 0 0 /dev/fd0 /media/floppy0 auto rw,user,noauto 0 0 # /dev/hdb1 /mnt/hd_slave auto user,rw 0 0 UUID=1db050f6-8895-41d9-9164-77d1aeb170db /mnt/hd_slave auto user,rw but it seems to me to be in order. lsmod: francesco@deb32:~$ lsmod Module Size Used by usb_storage 34951 0 uas 12975 0 mperf 12387 0 speedstep_lib 12463 0 cpufreq_powersave 12422 0 cpufreq_stats 12670 0 cpufreq_conservative 12987 0 cpufreq_userspace 12520 0 ppdev 12621 0 lp 12858 0 fuse 55666 1 nfsd 196206 2 nfs 219235 0 lockd 60891 2 nfsd,nfs fscache 31438 1 nfs auth_rpcgss
failure of gnome baker
In my updated debian i386 sqeeze/gnome and debian amd64 lenny/gnome i have no more workable cd-dvd burners. Gnome-baker reports burning (CD data disk) OK, however the CD is unreadable. In contrast, k3b works fine for both CD and DVD data disks. However, installation of k3b apt-get update apt-get install k3b brought other problems in: --command k3b also started the viewer VMD, which had to be closed twice in order that k3b could be used. --On restarting the computer, gnome could no more be called and a RedHat window was brought in instead. I liked gnome for years, and I use certain gnome-specific scientific applications, such as GChempain. However I notice now that KDE has a much more versatile burner (k3b), even if gnome baker could be used. Also the pdf viewer okular (better that Adobe for certain scientific uses) is part of KDE and alleviated from having to install Adobe. I believe that gnome developers should consider these observations. Lukily, okular can be used without problems even in gnome. Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/aanlkti=skhcd6spxzspd_a9zwhdyxrdvqnfhpnonp...@mail.gmail.com
about cd/dvd burners
Hello: gnomebaker returns OK burned, however the CD (data) is unreadable (debian i386 squeeze). I tried brasero with same issues. The same with amd64. Finally I installed k3b on i386 squeeze,, getting fully functioning data CD and DV D. Unfortunately, k3b installs too much kde, preventing startx to launch gnome (a window from RedHat is called instead). Also, command 'k3b' calld VMD (a viewer package); until VMD is closed twice, k3b does not work. I had to --purge remove everything about k3b and kde. This means that I was unable - at this moment - to get a comfortable cd/dvd burner with debian-gnome. thanks for your attention Francesco Pietra Accademia Lucchese di Scienze Lettere e Arti I-55100 Lucca. email chiendar...@gmail.com or francesco.pie...@accademialucchese.it -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/aanlktimteh8l=myzg2cm+esylywbqbjmbdx+arjvp...@mail.gmail.com
Re: nvidia legacy driver//kernel 2.6.32 issues
Solved through LinuxQuestions forum. Forget about this thread. fp On Tue, Apr 6, 2010 at 4:46 PM, Francesco Pietra chiendar...@gmail.com wrote: Following apt-get dist-upgrade with debian squeeze i386, upgrading from kernel 2.6.30 to 2.6.32, the xserver was broken at startx because kernel compiled with gcc 4.3 while now gcc 4.4. I could only boot from previous 2.6.30 to have the xserver at startx. Following export CC=/usr/bin/gcc-4.3 I reinstalled the nvidia driver NVIDIA-Linux-x86-96.43.16-pk1.run for my GeForce2 MX200 (rev b2), the driver installed correctly and was reconfigured correctly according to the nvidia installer messages, though, again, it works for 2.6.30, not for 2.6.32. Please see below the relevant portion of /var/log/Xorg.0.log: # II) Loading /usr/lib/xorg/modules/drivers/nvidia_drv.so (II) Module nvidia: vendor=NVIDIA Corporation compiled for 4.0.2, module version = 1.0.0 Module class: X.Org Video Driver (II) NVIDIA dlloader X Driver 96.43.16 Thu Jan 28 16:02:25 PST 2010 (II) NVIDIA Unified Driver for all Supported NVIDIA GPUs (II) Primary Device is: PCI 0...@00:00:0 (II) Loading sub module fb (II) LoadModule: fb (II) Loading /usr/lib/xorg/modules/libfb.so (II) Module fb: vendor=X.Org Foundation compiled for 1.7.6, module version = 1.0.0 ABI class: X.Org ANSI C Emulation, version 0.4 (II) Loading sub module ramdac (II) LoadModule: ramdac (II) Module ramdac already built-in (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(0): RGB weight 888 (==) NVIDIA(0): Default visual is TrueColor (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(0): Enabling RENDER acceleration (II) NVIDIA(0): Support for GLX with the Damage and Composite X extensions is (II) NVIDIA(0): enabled. (EE) NVIDIA(0): Failed to load the NVIDIA kernel module! (EE) NVIDIA(0): *** Aborting *** (II) UnloadModule: nvidia (II) UnloadModule: fb (EE) Screen(s) found, but none have a usable configuration. # With previous 2.6.30 I used successfully either the debian way or the nvidia installer (actually, I remained at the nvidia installer installation of the driver). Now I am using the 2.6.30 kernel with the installation for 2.6.32, which is too bad. thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/u2lb87c422a1004070238v1b16046cye54f6733e6ad1...@mail.gmail.com
nvidia legacy driver//kernel 2.6.32 issues
Following apt-get dist-upgrade with debian squeeze i386, upgrading from kernel 2.6.30 to 2.6.32, the xserver was broken at startx because kernel compiled with gcc 4.3 while now gcc 4.4. I could only boot from previous 2.6.30 to have the xserver at startx. Following export CC=/usr/bin/gcc-4.3 I reinstalled the nvidia driver NVIDIA-Linux-x86-96.43.16-pk1.run for my GeForce2 MX200 (rev b2), the driver installed correctly and was reconfigured correctly according to the nvidia installer messages, though, again, it works for 2.6.30, not for 2.6.32. Please see below the relevant portion of /var/log/Xorg.0.log: # II) Loading /usr/lib/xorg/modules/drivers/nvidia_drv.so (II) Module nvidia: vendor=NVIDIA Corporation compiled for 4.0.2, module version = 1.0.0 Module class: X.Org Video Driver (II) NVIDIA dlloader X Driver 96.43.16 Thu Jan 28 16:02:25 PST 2010 (II) NVIDIA Unified Driver for all Supported NVIDIA GPUs (II) Primary Device is: PCI 0...@00:00:0 (II) Loading sub module fb (II) LoadModule: fb (II) Loading /usr/lib/xorg/modules/libfb.so (II) Module fb: vendor=X.Org Foundation compiled for 1.7.6, module version = 1.0.0 ABI class: X.Org ANSI C Emulation, version 0.4 (II) Loading sub module ramdac (II) LoadModule: ramdac (II) Module ramdac already built-in (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(0): RGB weight 888 (==) NVIDIA(0): Default visual is TrueColor (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(0): Enabling RENDER acceleration (II) NVIDIA(0): Support for GLX with the Damage and Composite X extensions is (II) NVIDIA(0): enabled. (EE) NVIDIA(0): Failed to load the NVIDIA kernel module! (EE) NVIDIA(0): *** Aborting *** (II) UnloadModule: nvidia (II) UnloadModule: fb (EE) Screen(s) found, but none have a usable configuration. # With previous 2.6.30 I used successfully either the debian way or the nvidia installer (actually, I remained at the nvidia installer installation of the driver). Now I am using the 2.6.30 kernel with the installation for 2.6.32, which is too bad. thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/x2zb87c422a1004060746vd49c2155w56727986b8267...@mail.gmail.com
Fwd: nvidia legacy driver//kernel 2.6.32 issues
Please see at bottom the successful log for 2.6.30 kernel. The difference is at line 122. I do not understand why even the log for 2/5/32 says first that the nvidia module was loaded and then (line 122) that it can't be found -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Tue, Apr 6, 2010 at 4:46 PM Subject: nvidia legacy driver//kernel 2.6.32 issues To: debian-users debian-user@lists.debian.org Following apt-get dist-upgrade with debian squeeze i386, upgrading from kernel 2.6.30 to 2.6.32, the xserver was broken at startx because kernel compiled with gcc 4.3 while now gcc 4.4. I could only boot from previous 2.6.30 to have the xserver at startx. Following export CC=/usr/bin/gcc-4.3 I reinstalled the nvidia driver NVIDIA-Linux-x86-96.43.16-pk1.run for my GeForce2 MX200 (rev b2), the driver installed correctly and was reconfigured correctly according to the nvidia installer messages, though, again, it works for 2.6.30, not for 2.6.32. Please see below the relevant portion of /var/log/Xorg.0.log: # II) Loading /usr/lib/xorg/modules/drivers/nvidia_drv.so (II) Module nvidia: vendor=NVIDIA Corporation compiled for 4.0.2, module version = 1.0.0 Module class: X.Org Video Driver (II) NVIDIA dlloader X Driver 96.43.16 Thu Jan 28 16:02:25 PST 2010 (II) NVIDIA Unified Driver for all Supported NVIDIA GPUs (II) Primary Device is: PCI 0...@00:00:0 (II) Loading sub module fb (II) LoadModule: fb (II) Loading /usr/lib/xorg/modules/libfb.so (II) Module fb: vendor=X.Org Foundation compiled for 1.7.6, module version = 1.0.0 ABI class: X.Org ANSI C Emulation, version 0.4 (II) Loading sub module ramdac (II) LoadModule: ramdac (II) Module ramdac already built-in (**) NVIDIA(0): Depth 24, (--) framebuffer bpp 32 (==) NVIDIA(0): RGB weight 888 (==) NVIDIA(0): Default visual is TrueColor (==) NVIDIA(0): Using gamma correction (1.0, 1.0, 1.0) (**) NVIDIA(0): Enabling RENDER acceleration (II) NVIDIA(0): Support for GLX with the Damage and Composite X extensions is (II) NVIDIA(0): enabled. (EE) NVIDIA(0): Failed to load the NVIDIA kernel module! (EE) NVIDIA(0): *** Aborting *** (II) UnloadModule: nvidia (II) UnloadModule: fb (EE) Screen(s) found, but none have a usable configuration. # With previous 2.6.30 I used successfully either the debian way or the nvidia installer (actually, I remained at the nvidia installer installation of the driver). Now I am using the 2.6.30 kernel with the installation for 2.6.32, which is too bad. thanks francesco pietra Xorg.0.log for 2.6.30 kernel: X.Org X Server 1.7.6 Release Date: 2010-03-17 X Protocol Version 11, Revision 0 Build Operating System: Linux 2.6.32.10-dsa-ia32 i686 Debian Current Operating System: Linux deb32 2.6.30-1-686 #1 SMP Sat Aug 15 19:11:58 UTC 2009 i686 Kernel command line: root=/dev/mapper/deb32-root ro quiet Build Date: 23 March 2010 10:07:02PM xorg-server 2:1.7.6-1 (Cyril Brulebois k...@debian.org) Current version of pixman: 0.16.4 Before reporting problems, check http://wiki.x.org to make sure that you have the latest version. Markers: (--) probed, (**) from config file, (==) default setting, (++) from command line, (!!) notice, (II) informational, (WW) warning, (EE) error, (NI) not implemented, (??) unknown. (==) Log file: /var/log/Xorg.0.log, Time: Tue Apr 6 16:17:58 2010 (==) Using config file: /etc/X11/xorg.conf (==) ServerLayout Layout0 (**) |--Screen Screen0 (0) (**) | |--Monitor Monitor0 (**) | |--Device Device0 (**) |--Input Device Keyboard0 (**) |--Input Device Mouse0 (==) Automatically adding devices (==) Automatically enabling devices (WW) The directory /usr/share/fonts/X11/cyrillic does not exist. Entry deleted from font path. (==) FontPath set to: /usr/share/fonts/X11/misc, /usr/share/fonts/X11/100dpi/:unscaled, /usr/share/fonts/X11/75dpi/:unscaled, /usr/share/fonts/X11/Type1, /usr/share/fonts/X11/100dpi, /usr/share/fonts/X11/75dpi, /var/lib/defoma/x-ttcidfont-conf.d/dirs/TrueType, built-ins (==) ModulePath set to /usr/lib/xorg/modules (WW) AllowEmptyInput is on, devices using drivers 'kbd', 'mouse' or 'vmmouse' will be disabled. (WW) Disabling Keyboard0 (WW) Disabling Mouse0 (II) Loader magic: 0x81e7be0 (II) Module ABI versions: X.Org ANSI C Emulation: 0.4 X.Org Video Driver: 6.0 X.Org XInput driver : 7.0 X.Org Server Extension : 2.0 (--) using VT number 7 (--) PCI:*(0:1:0:0) 10de:0111:: nVidia Corporation NV11DDR [GeForce2 MX200] rev 178, Mem @ 0xec00/16777216, 0xe000/134217728, BIOS @ 0x/65536 (II) Open ACPI successful (/var/run/acpid.socket) (II) LoadModule: extmod (II) Loading /usr/lib/xorg/modules/extensions/libextmod.so (II) Module extmod: vendor=X.Org Foundation compiled for 1.7.6, module version = 1.0.0 Module class: X.Org Server Extension ABI class: X.Org Server Extension, version
Re: what about acroread in squeeze i386?
Unfortunately, for dealing with most editors of scientific journals, and for personal use of the scientific literature, either as author or referee, neither the readers you mention, nor any one other I know except acroread, are enough. Because of these problems (which are not unique to acroread), most my colleagues have turned to either Microsoft or Apple for the desktop. I intend to stick to Debian also for the desktop, but such affairs are wasting our time. We can not devote more time to have acroread running than for a scientific code. At present, the second task has become easier that the trivial affair of having office tools running. I am also surprised about the Debian policy for deb packages of scientific code: they provide the last version for testing or sid, while scientific code is run on stable Debian. So, the developer do much work for nothing. This criticism is intended to be constructive, so that I have extended this reply to Debian and Vincenzo, who kindly tried to help. Have a nice day francesco On Mon, Mar 1, 2010 at 12:40 AM, Jameson Rollins jroll...@finestructure.net wrote: On Sun, 28 Feb 2010 19:30:32 +0100, Francesco Pietra chiendar...@gmail.com wrote: What about acroread in squeeze i386? The only reason here to maintain a computer with squeeze is to provide a needed tool to scientists. Why acroread acroread-mozilla acroread-plugins can't be found on debian-multimedia i386 squeeze/testing? We have to run more expensive and more energy demanding 64-bit machines with lenny to have such packages. Curious about the reason why squeeze has no efficient pdf reader. There are plenty of very good free pdf readers in squeeze: evince xpdf konqueror jamie. -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/b87c422a1003010008j6f85fb6eo757594de596b3...@mail.gmail.com
what about acroread in squeeze i386?
What about acroread in squeeze i386? The only reason here to maintain a computer with squeeze is to provide a needed tool to scientists. Why acroread acroread-mozilla acroread-plugins can't be found on debian-multimedia i386 squeeze/testing? We have to run more expensive and more energy demanding 64-bit machines with lenny to have such packages. Curious about the reason why squeeze has no efficient pdf reader. thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/b87c422a1002281030k46e3214tf012b696a121e...@mail.gmail.com
failure to reinstall boot and root
Following a major mistake (I deleted /lib, while it was intended to delete lib of an application) I am trying to restore my amd64 lenny via netinstall, downloading the Jan 2010 amd64 lenny CD. Not touching the many applications installed in usr and opt and data in home. The situation arising, after editing for what I intended to format and install ex novo (/boot, /, and swap): LVM VG vg1 LV home #1 LVM VG vg1 LV opt #1 LVM VG vg1 LV F swap swap #1 LVM VG vg1 LV tmp #1 LVM VG vg1 LV usr #1 LVM VG vg1 LV var #1 RAID1 device #0 F ext 2 /boot RAID1 device #1 F ext 3 / RAID1 device #2 K lvm SCSI3 (0,0,0) (sda) 250 GB #1 primary 197 MB B K raid #2 primary 1GB K raid #3 primary 248GB K raid pri.log 855MB free space SCSI4 (0,0,0) (sdb) 250MB same as sda (all ext 3 except boot ext2, with formatting /boot and / only) I choose a mirror, installing *Desktop environment *Standard system It hangs at retrieving file 609 of 794 Select and install software failed. Also grub installing failed. Clearly, I was following a wrong path. I would appreciate advice how to restore the system, if still possible saving the applications in usr and opt, now that /boot, /, and swap have been formatted. Previously, I installed by formatting everything of the above scheme. Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/b87c422a1002220746k7b6c539kc882b4b1c4b07...@mail.gmail.com
gfax issues squeeze i386
Installed gfax on Debian Linux i386 squeeze. Also installed: libc-bin libc-dev-bin libpaper-utils. Also upgraded: libc6 libc6-dev libc6-i686 libmono-corlib2.0-cil libmono-security2.0-cil libmono-system2.0-cil locales mono-2.0-gac mono-gac mono-runtime. It fails to work. As user: france...@deb32:~$ gfax Unhandled Exception: System.UnauthorizedAccessException: Access to the path /var/spool/gfax is denied. at System.IO.Directory.CreateDirectoriesInternal (System.String path) [0x0] at System.IO.Directory.CreateDirectory (System.String path) [0x0] at System.IO.DirectoryInfo.Create () [0x0] at (wrapper remoting-invoke-with-check) System.IO.DirectoryInfo:Create () at System.IO.Directory.CreateDirectoriesInternal (System.String path) [0x0] at System.IO.Directory.CreateDirectory (System.String path) [0x0] at gfax.gfax.Main (System.String[] args) [0x0] france...@deb32:~$ ... As superuser: deb32:/home/francesco# gfax (/usr/lib/gfax/gfax.exe:2801): GLib-GObject-CRITICAL **: /build/buildd-glib2.0_2.22.4-1-i386-jRfNZE/glib2.0-2.22.4/gobject/gtype.c:2458: initialization assertion failed, use IA__g_type_init() prior to this function (/usr/lib/gfax/gfax.exe:2801): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (/usr/lib/gfax/gfax.exe:2801): GLib-GObject-CRITICAL **: g_object_ref: assertion `G_IS_OBJECT (object)' failed Stacktrace: at (wrapper managed-to-native) GConf.Client.gconf_client_get_default () 0x4 at (wrapper managed-to-native) GConf.Client.gconf_client_get_default () 0x at GConf.Client..ctor () 0x00046 at gfax.Settings..cctor () 0x00026 at (wrapper runtime-invoke) object.runtime_invoke_void (object,intptr,intptr,intptr) 0x at gfax.gfax.Main (string[]) 0x at gfax.gfax.Main (string[]) 0x004c4 at (wrapper runtime-invoke) gfax.gfax.runtime_invoke_void_object (object,intptr,intptr,intptr) 0x Native stacktrace: mono [0x80c9089] mono [0x80f3f13] [0xb801e40c] /usr/lib/libgconf-2.so.4(gconf_client_get_default+0xf8) [0xb7043c98] [0xb79642ce] [0xb796417f] [0xb7964117] [0xb795b2ba] mono [0x811058a] mono [0x80866f1] mono [0x8061358] mono [0x8062b38] mono [0x80d1a76] [0xb800d066] [0xb795b203] mono(mono_runtime_exec_main+0xde) [0x810edae] mono(mono_runtime_run_main+0x15a) [0x810f52a] mono(mono_main+0x1a4d) [0x80b187d] mono [0x805aab5] /lib/i686/cmov/libc.so.6(__libc_start_main+0xe5) [0xb7dd3b55] mono [0x805a9f1] Debug info from gdb: = Got a SIGSEGV while executing native code. This usually indicates a fatal error in the mono runtime or one of the native libraries used by your application. = /usr/bin/gfax: line 37: 2801 Aborted mono /usr/lib/gfax/gfax.exe $@ deb32:/home/francesco# Thanks for help francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Fwd: gfax issues squeeze i386
Following mkdir /var/spool/gfax/francesco command gfax as user francesco opens the fax window for an instant only, such as for a segmentaion fault. Nothing on the console from which the command gfax was issued. francesco -- Forwarded message -- From: Francesco Pietra chiendar...@gmail.com Date: Sat, Feb 13, 2010 at 9:00 AM Subject: gfax issues squeeze i386 To: debian-users debian-user@lists.debian.org Installed gfax on Debian Linux i386 squeeze. Also installed: libc-bin libc-dev-bin libpaper-utils. Also upgraded: libc6 libc6-dev libc6-i686 libmono-corlib2.0-cil libmono-security2.0-cil libmono-system2.0-cil locales mono-2.0-gac mono-gac mono-runtime. It fails to work. As user: france...@deb32:~$ gfax Unhandled Exception: System.UnauthorizedAccessException: Access to the path /var/spool/gfax is denied. at System.IO.Directory.CreateDirectoriesInternal (System.String path) [0x0] at System.IO.Directory.CreateDirectory (System.String path) [0x0] at System.IO.DirectoryInfo.Create () [0x0] at (wrapper remoting-invoke-with-check) System.IO.DirectoryInfo:Create () at System.IO.Directory.CreateDirectoriesInternal (System.String path) [0x0] at System.IO.Directory.CreateDirectory (System.String path) [0x0] at gfax.gfax.Main (System.String[] args) [0x0] france...@deb32:~$ ... As superuser: deb32:/home/francesco# gfax (/usr/lib/gfax/gfax.exe:2801): GLib-GObject-CRITICAL **: /build/buildd-glib2.0_2.22.4-1-i386-jRfNZE/glib2.0-2.22.4/gobject/gtype.c:2458: initialization assertion failed, use IA__g_type_init() prior to this function (/usr/lib/gfax/gfax.exe:2801): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (/usr/lib/gfax/gfax.exe:2801): GLib-GObject-CRITICAL **: g_object_ref: assertion `G_IS_OBJECT (object)' failed Stacktrace: at (wrapper managed-to-native) GConf.Client.gconf_client_get_default () 0x4 at (wrapper managed-to-native) GConf.Client.gconf_client_get_default () 0x at GConf.Client..ctor () 0x00046 at gfax.Settings..cctor () 0x00026 at (wrapper runtime-invoke) object.runtime_invoke_void (object,intptr,intptr,intptr) 0x at gfax.gfax.Main (string[]) 0x at gfax.gfax.Main (string[]) 0x004c4 at (wrapper runtime-invoke) gfax.gfax.runtime_invoke_void_object (object,intptr,intptr,intptr) 0x Native stacktrace: mono [0x80c9089] mono [0x80f3f13] [0xb801e40c] /usr/lib/libgconf-2.so.4(gconf_client_get_default+0xf8) [0xb7043c98] [0xb79642ce] [0xb796417f] [0xb7964117] [0xb795b2ba] mono [0x811058a] mono [0x80866f1] mono [0x8061358] mono [0x8062b38] mono [0x80d1a76] [0xb800d066] [0xb795b203] mono(mono_runtime_exec_main+0xde) [0x810edae] mono(mono_runtime_run_main+0x15a) [0x810f52a] mono(mono_main+0x1a4d) [0x80b187d] mono [0x805aab5] /lib/i686/cmov/libc.so.6(__libc_start_main+0xe5) [0xb7dd3b55] mono [0x805a9f1] Debug info from gdb: = Got a SIGSEGV while executing native code. This usually indicates a fatal error in the mono runtime or one of the native libraries used by your application. = /usr/bin/gfax: line 37: 2801 Aborted mono /usr/lib/gfax/gfax.exe $@ deb32:/home/francesco# Thanks for help francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
warning about nautilus and brasero
With my debian squeeze i386 (upgraded to yesterday) calling nautilus and trying to workout Preferences, removes all icons from the gnome desktop. I reenter as user and installed brasero with # apt-get install brasero without paying much attention to what was going on. Well, the X-system was removed. I had to reinstall, and reconfigure, X. francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
failure to upgrade linux-image squeeze
Hi: Upgraded i386 from lenny to squeeze. OK, except for (from several days) on apt-get upgrade errors with linux-image-2,6.301-686-2.6.30-6_i386.deb Following with apt-get -f install probably is a remedy, but why any time? am I alone with such an issue? francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Repeating Debian icon on gnome panel
My old K7S5A/SIS735/Athlon/i386 debian lenny, now upgraded to squeeze (no 3D graphics), has developed a tendency to repeat unasked commands when in gnome, or console in gnome. No problems using the Debian console without starting gnome. This has installed a number of unmovable Debian icons in the gnome panel, each icon functioning for main menu, while the gnome foot has disappeared. Neither dmesg nor lshw or lspci from the debian console, without starting gnome, reveal - to my eyes - any hardware failure. I use this old stuff for scp communication with computing clusters or UMA. Upgrading to squeeze, gnome 26, did not help. Grateful for suggestions how to remedy or decide to replace the desktop (actually i asked yesterday for advice on mainboards and i received advice; now i am trying to resuscitate the desktop to save time; otherwise i have a couple of Raptors for a new sata mainboard) thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
motherboad for desktop
Hi: My old K7S5A (SiS735 chipset) Athlon i386 lenny desktop has died and I am wondering how to set up a new one for the same service (running 32bit graphic scientific programs, besides office use, and establishing scp connection with my amd64 computing machines). Absolutely no need of multicore, rather, a single fast processor would be of use for scientific purposes as parallelized codes are rare stuff. I thought to by a second hand single-processor motherboard but it might result as a bad jump into the past. Also, I have a couple of unused 150GB Raptor WD HDs that could only be used if nthe motherboard has SATA connections (better two, so as to set up a RAID1). Any suggestion on which motherboard (or motherboard type if you prefer to be uncommittal about brand) would be greatly appreciated. Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
X11 issue
Hi: Following the lines of successful setup of 3D nvidia driver with lenny amd64, i met failure with lenny i386 on a old K7S5A Elite mainboard with NV11DDR (GeForce2 MX200 rev b2). I also lost OpenGL, which I used for several applications. What i did: # apt-get install nvidia-kernel-common module-assistant # m-a -i -t prepare # m-a clean,a-i -i -t -f nvidia-kernel-source # depmod -a # apt-get install nvidia-glx nvidia-glx-dev mesa-utils # dpkg-reconfigure xserver-xorg (no X on reboot) # dpkg-reconfigure -phogh xserver-xorg (X yes, bot no nvidia driver.) Then I edited /etc/X11/xorg.conf, adding ' Driver nvidia ' 'to the ' Section Device ', which worked with amd64 but not here (no more X) to regin X, I could either command # dexconf which removed the line ' Driver nvidia ' , or replace with ' Driver nv ' but in either case no more OpenGl, although libmotif3 is installed. When trying to launch the scientific viewer Chimera, the error: File CHIMERA/share/chimera/tkgui.py, line 2525, in initializeGUI File /usr/local/chimera/lib/python2.5/site-packages/PIL/__init__.py, line 309, in checkConfig File /usr/local/chimera/lib/python2.5/site-packages/Togl.py, line 27, in __init__ Tkinter.Widget.__init__(self, master, togl, cnf, kw) File /usr/local/chimera/lib/python2.5/lib-tk/Tkinter.py, line 1930, in __init__ (widgetName, self._w) + extra + self._options(cnf)) _tkinter.TclError: X server has no OpenGL GLX extension Couldn't configure togl widget An inquiry about nvidia reports: dpkg -l '*nvidia*' Desired=Unknown/Install/Remove/Purge/Hold | Status=Not/Inst/Cfg-files/Unpacked/Failed-cfg/Half-inst/trig-aWait/Trig-pend |/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad) ||/ Name VersionDescription +++-==-==- ii nvidia-glx 173.14.09-5NVIDIA binary Xorg driver ii nvidia-glx-dev 173.14.09-5NVIDIA binary Xorg driver development files un nvidia-glx-src none (no description available) un nvidia-kernel- none (no description available) ii nvidia-kernel- 173.14.09-5+2. NVIDIA binary kernel module for Linux 2.6.26 ii nvidia-kernel- 20080825+1 NVIDIA binary kernel module common files ii nvidia-kernel- 173.14.09-5NVIDIA binary kernel module source un nvidia-kernel- none (no description available) un nvidia-setting none (no description available) Thanks for advice francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
both bootable in raid1
Hi: I am looking for a debian thread instructing how to make bootable both disks in a mdadm raid1. I followed successfully the recipe time ago, don't remember how, and unfortunately i did not take notice of. Unable now to find the thread on the web. But I am sure there is and I need to reapply the recipe. Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
removing X
Hi: May I ask advice to remove completely X - without leaving broken packages - from a multisocket server running on debian amd64 lenny, kernel 2.6.26? Is it enough to purge remove the packages xorg and xbase-clients? Does the likely presence of corrupted X files hinder a clean unistalling? Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
XIO: fatal error 104
Hi: I have little familiarity with X11, in particular on my computing multisocket with amd64 lenny, where it is seldom used. Now that it is needed, it does not work any more. Command startx or X (as user) reports: X.Org X Server 1.4.2 Release Date: 11 June 2008 X Protocol Version 11, Revision 0 Build Operating System: Linux Debian (xorg-server 2:1.4.2-10) Current Operating System: Linux deb64 2.6.24-1-amd64 #1 SMP Sat May 10 09:28:10 UTC 2008 x86_64 Build Date: 09 January 2009 02:16:05AM Before reporting problems, check http://wiki.x.org to make sure that you have the latest version. Module Loader present Markers: (--) probed, (**) from config file, (==) default setting, (++) from command line, (!!) notice, (II) informational, (WW) warning, (EE) error, (NI) not implemented, (??) unknown. (==) Log file: /var/log/Xorg.0.log, Time: Sun Jan 25 15:47:02 2009 (==) Using config file: /etc/X11/xorg.conf (II) Module ddc already built-in (II) Module ddc already built-in (II) Module ramdac already built-in (II) Module i2c already built-in Backtrace: 0: /usr/bin/X11/X(xf86SigHandler+0x6a) [0x48dd0a] 1: /lib/libc.so.6 [0x2ab82827df60] Fatal server error: Caught signal 11. Server aborting XIO: fatal IO error 104 (Connection reset by peer) on X server :0.0 after 0 requests (0 known processed) with 0 events remaining. = Other information: (WW) The directory /usr/X11R6/lib/X11/fonts/misc does not exist. (WW) The directory /usr/share/fonts/X11/cyrillic does not exist. (WW) The directory /usr/X11R6/lib/X11/fonts/cyrillic does not exist. (WW) The directory /usr/X11R6/lib/X11/fonts/100dpi/ does not exist. (WW) The directory /usr/X11R6/lib/X11/fonts/75dpi/ does not exist. (WW) The directory /usr/X11R6/lib/X11/fonts/Type1 does not exist. (WW) The directory /usr/X11R6/lib/X11/fonts/100dpi does not exist. (WW) The directory /usr/X11R6/lib/X11/fonts/75dpi does not exist. (WW) The directory /var/lib/defoma/x-ttcidfont-conf.d/dirs/TrueType does not exist. (WW) MACH64(0): Cannot shadow an accelerated frame buffer. Section Module Loadbitmap Loadddc Loaddri Loadextmod Loadfreetype Loadglx Loadint10 Loadvbe EndSection Section Device Identifier ATI Technologies Inc Rage XL Driver ati BusID PCI:3:1:0 EndSection = 03:01.0 VGA compatible controller: ATI Technologies Inc Rage XL (rev 27) === I tried #dpkg-reconfigure xserver -xorg setting: kernel framebuffer device interface: yes Keyboard layout: pc104 but id did not help. Thanks for helping francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Failure of a deb package installation
Hi: As no clues arrive from the package web site, may I ask if the following problems may derive from my bad management of the OS? Task: install octopus on a multisocket dual-opteron 875, OS = debian amd64 lenny (octopus is a molecular computational program). 1) downloaded octopus-3.0.1-1.x86_64.rpm. 2) #alien -k --scripts octopus-3.0.1-1.x86_64.rpm (which reported no errors). 3) #dpkg -i octopus-3.0.1-1.x86_64.deb Selecting previous deselected package octopus. (Reading database ... 106160 files and directories currently installed). Unpacking octopus (from octopus-3.0.1-1.x86_64.deb) ... Setting up octopus (3.0.1-1) ... dpkg: error processing octopus (--install): subprocess post-installation script returned error exit status 2 Processing triggers for man-db ... Errors were encountered while processing: octopus == Subsequently, on command # apt-get update #apt-get upgrade 1 not fully installed or removed. Setting up octopus (3.0.1-1) ... dpkg: error processing octopus (--configure) subprocess post-installation script returned error exit status 2 E: Sub-process /usr/bin/dpkg returned an error code (1) === Command #apt-get -f install reports now the same error. == Is that an error in the configuration of the program? Thanks for help francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
ssh
Hi: Is any 'send file' command to make so that two machines (an amd64 multisocket and a simple i386, both lenny) talk scp with one another through a router (attached to adsl) fully without asking the password? With 'fully' I mean that command: ssh target_machine_name date gives the date without asking a password. The mere sending id_rsa.pub to create the authorized_keys file only works (without asking the password) for command: ssh target_machine_name but if 'date' is also requested, the password is needed (at least in my hands). I know how to solve the issue, i.e. by cross appending the authorized_keys files, in order that each machine knows itself. But there must be a simpler way. Why that need? Certain parallelized computational codes only work if the above 'fully' is met. I came once again across the issue in reinstalling i386 following a died HD. Thanks francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Fwd: Failure to load amd64 overcome, though mem problems
Posted again from the e-mail address I am registered to -- Forwarded message -- From: Francesco Pietra francesco.pie...@accademialucchese.it Date: Fri, Jan 2, 2009 at 8:26 PM Subject: Failure to load amd64 overcome, though mem problems To: amd64 Debian debian-am...@lists.debian.org, debian-users debian-user@lists.debian.org Hi: Near the end of last year, in a period of vacation, I posted to amd64 about failure to start amd64 lenny with a Supermicro H8QC8 motherboard. This board has chipset nVidia CK804, which is also memory controller, and AMD 8132. It bears 4 dual opteron 875 CPUs, two WD Raptor under RAID as well as 8 KVR400D4R3A/2G and 8 KVR400D4R3A/1G. Lenny is set not to load the X system. The computer is powered through an APC 1500 and Enermax EGX1000EWL. Cooling is extremely efficient. The system was shut down correctly when top indicated 24GB total RAM. After a few days untouched, the OS did not load, the screen showing a series of lines starting with RDX RBP R10 R13 FS CS CR2 DR0 DR3, followed by Call Trace: do_oage fff handle_mm_fault fff vma_link fff error_exit fff clear_user fff padzero fff get_arg_page fff copy_strings fff search_binary_handler fffdo_execve fff sys_execve fff stub_execve After that such lines alternate, and the whole Call Trace started several times anew, everything disappeared from the screen and could not be recovered with the keyboard. Knoppix 5.3.1 loaded correctly, detected all 8 logical CPUs, the raid1 partitions (mdadm) were OK, however it detected 20GB total mem, instead of the 24GB expected. memtest86+-2.11 detected 17GB total mem and was let to run for the whole 8 cycles (which took seven hours), reporting no mem errors. DMI mem device info showed: DIMM 0 to DIMM 7: size 64; speed 400; type DDR DIMM 8 to DIMM 10: size empty; speed 200; type DDR DIMM 11: size 2048; speed 200; type DDR DIMM 12 to DIMM 15: size 64; speed 200; type DDR. On rebooting, lenny started correctly. Top showed 18079572k total, also when running a parallelized application that engaged all 8 CPUs. lshw agreed with memtest as to the DIMMs, except for the one marked of size = 2048, which lshw marked of size=64. I was surprised that half of the slots were indicated by both memtest and lshw at speed=200; I tentatively assume this is a feature of the mainboard not of the mem slots. = The actual mem size is insufficient for my computations and the empty DIMMs need attention I believe. There is no system maintainer here and I have to try to restore the system alone, also because I assembled the computer. My question is from where to start at this point. The mem slots seem to be plugged in as before but I did not try to remove and replug. The four blocks on the mainboard were filled as follows: DIMMA-2A 1GB DIMMA-2B 1GB DIMMA-1A 2GB DIMMA-1B 2GB DIMMB-1B 2GB DIMMB-1A 2GB DIMMB-2B 1GB DIMMB-2A 1GB DIMMC-2A 1GB DIMMC-2B 1GB DIMMC-1A 2GB DIMMC-1B 2GB DIMMD-1B 2GB DIMMD-1A 2GB DIMMD-2B 1GB DIMMD-2A 1GB = This mail started originally under the hypothesis that the problem was some degradation of lenny. I understand now that this mail is largely out of topic both on amd64 and users. Hope only that experienced users may suggest from their experience. Thanks and happy 2009! francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Failure to load amd64 overcome, though mem problems
Hi: Near the end of last year, in a period of vacation, I posted to amd64 about failure to start amd64 lenny with a Supermicro H8QC8 motherboard. This board has chipset nVidia CK804, which is also memory controller, and AMD 8132. It bears 4 dual opteron 875 CPUs, two WD Raptor under RAID as well as 8 KVR400D4R3A/2G and 8 KVR400D4R3A/1G. Lenny is set not to load the X system. The computer is powered through an APC 1500 and Enermax EGX1000EWL. Cooling is extremely efficient. The system was shut down correctly when top indicated 24GB total RAM. After a few days untouched, the OS did not load, the screen showing a series of lines starting with RDX RBP R10 R13 FS CS CR2 DR0 DR3, followed by Call Trace: do_oage fff handle_mm_fault fff vma_link fff error_exit fff clear_user fff padzero fff get_arg_page fff copy_strings fff search_binary_handler fffdo_execve fff sys_execve fff stub_execve After that such lines alternate, and the whole Call Trace started several times anew, everything disappeared from the screen and could not be recovered with the keyboard. Knoppix 5.3.1 loaded correctly, detected all 8 logical CPUs, the raid1 partitions (mdadm) were OK, however it detected 20GB total mem, instead of the 24GB expected. memtest86+-2.11 detected 17GB total mem and was let to run for the whole 8 cycles (which took seven hours), reporting no mem errors. DMI mem device info showed: DIMM 0 to DIMM 7: size 64; speed 400; type DDR DIMM 8 to DIMM 10: size empty; speed 200; type DDR DIMM 11: size 2048; speed 200; type DDR DIMM 12 to DIMM 15: size 64; speed 200; type DDR. On rebooting, lenny started correctly. Top showed 18079572k total, also when running a parallelized application that engaged all 8 CPUs. lshw agreed with memtest as to the DIMMs, except for the one marked of size = 2048, which lshw marked of size=64. I was surprised that half of the slots were indicated by both memtest and lshw at speed=200; I tentatively assume this is a feature of the mainboard not of the mem slots. = The actual mem size is insufficient for my computations and the empty DIMMs need attention I believe. There is no system maintainer here and I have to try to restore the system alone, also because I assembled the computer. My question is from where to start at this point. The mem slots seem to be plugged in as before but I did not try to remove and replug. The four blocks on the mainboard were filled as follows: DIMMA-2A 1GB DIMMA-2B 1GB DIMMA-1A 2GB DIMMA-1B 2GB DIMMB-1B 2GB DIMMB-1A 2GB DIMMB-2B 1GB DIMMB-2A 1GB DIMMC-2A 1GB DIMMC-2B 1GB DIMMC-1A 2GB DIMMC-1B 2GB DIMMD-1B 2GB DIMMD-1A 2GB DIMMD-2B 1GB DIMMD-2A 1GB = This mail started originally under the hypothesis that the problem was some degradation of lenny. I understand now that this mail is largely out of topic both on amd64 and users. Hope only that experienced users may suggest from their experience. Thanks and happy 2009! francesco pietra -- To UNSUBSCRIBE, email to debian-user-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Re: Disk /dev/md6 doesn't contain valid partition table
On Wed, Oct 29, 2008 at 7:06 AM, Douglas A. Tutty [EMAIL PROTECTED] wrote: On Wed, Oct 29, 2008 at 05:44:31AM +0100, Francesco Pietra wrote: Major mistake (shutting down the ups unit) while doing a parallel computation on all 8 processors (UMA-type machine amd64 lenny with raid 1 two disks). On restarting the machine and the computation, fdisk -l showed Disk /dev/md6 doesn't contain a valid partition table df -h showed 97G 1.1G 91G 2% /home (which should have been ca 70% used). All other partitions were OK, as they should be. It would help us to follow if you provided a map of device to mount-point since, e.g. whe don't know what device is /home. As from my raid1 setup documantation: md 6 is /home/francesco/ md5 is /tmp Any command to check the above from the present status? In present status; cat /proc/mdstat: Personalities : [raid1] md6 : active raid1 sda8[0] sdb8[1] 102341952 blocks [2/2] [UU] md5 : active raid1 sda7[0] sdb7[1] 1951744 blocks [2/2] [UU] md4 : active raid1 sda6[0] sdb6[1] 2931712 blocks [2/2] [UU] md3 : active raid1 sda5[0] sdb5[1] 14651136 blocks [2/2] [UU] md1 : active(auto-read-only) raid1 sda2[0] sdb2[1] 6835584 blocks [2/2] [UU] md0 : active raid1 sda1[0] sdb1[1] 2931712 blocks [2/2] [UU] md2 : active raid1 sda3[0] sdb3[1] 14651200 blocks [2/2] [UU] unused devices: none = fdisk -l: Disk /dev/sda: 150.0 GB, 150039945216 bytes 255 heads, 63 sectors/track, 18241 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Disk identifier: 0x0009e776 Device Boot Start End Blocks Id System /dev/sda1 * 1 365 2931831 fd Linux raid autodetect /dev/sda2 3661216 6835657+ fd Linux raid autodetect /dev/sda31217304014651280 fd Linux raid autodetect /dev/sda43041 18213 121877122+ 5 Extended /dev/sda53041486414651248+ fd Linux raid autodetect /dev/sda648655229 2931831 fd Linux raid autodetect /dev/sda752305472 1951866 fd Linux raid autodetect /dev/sda85473 18213 102342051 fd Linux raid autodetect Disk /dev/sdb: 150.0 GB, 150039945216 bytes 255 heads, 63 sectors/track, 18241 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Disk identifier: 0x000b05ba Device BootDisk /dev/md2 doesn't contain a valid partition table Disk /dev/md0 doesn't contain a valid partition table Start End Blocks Id System /dev/sdb1 * 1 365 2931831 fd Linux raid autodetect /dev/sdb2 3661216 6835657+ fd Linux raid autodetect /dev/sdb31217304014651280 fd Linux raid autodetect /dev/sdb43041 18213 121877122+ 5 Extended /dev/sdb53041486414651248+ fd Linux raid autodetect /dev/sdb648655229 2931831 fd Linux raid autodetect /dev/sdb752305472 1951866 fd Linux raid autodetect /dev/sdb85473 18213 102342051 fd Linux raid autodetect Disk /dev/md2: 15.0 GB, 15002828800 bytes 2 heads, 4 sectors/track, 3662800 cylinders Units = cylinders of 8 * 512 = 4096 bytes Disk identifier: 0x Disk /dev/md0: 3002 MB, 3002073088 bytes 2 heads, 4 sectors/track, 732928 cylinders Units = cylinders of 8 * 512 = 4096 bytes Disk identifier: 0x Disk /dev/md1: 6999 MB, 6999638016 bytes 2 heads,Disk /dev/md1 doesn't contain a valid partition table Disk /dev/md3 doesn't contain a valid partition table Disk /dev/md4 doesn't contain a valid partition table Disk /dev/md5 doesn't contain a valid partition table Disk /dev/md6 doesn't contain a valid partition table 4 sectors/track, 1708896 cylinders Units = cylinders of 8 * 512 = 4096 bytes Disk identifier: 0x Disk /dev/md3: 15.0 GB, 15002763264 bytes 2 heads, 4 sectors/track, 3662784 cylinders Units = cylinders of 8 * 512 = 4096 bytes Disk identifier: 0x Disk /dev/md4: 3002 MB, 3002073088 bytes 2 heads, 4 sectors/track, 732928 cylinders Units = cylinders of 8 * 512 = 4096 bytes Disk identifier: 0x Disk /dev/md5: 1998 MB, 1998585856 bytes 2 heads, 4 sectors/track, 487936 cylinders Units = cylinders of 8 * 512 = 4096 bytes Disk identifier: 0x Disk /dev/md6: 104.7 GB, 104798158848 bytes 2 heads, 4 sectors/track, 25585488 cylinders Units = cylinders of 8 * 512 = 4096 bytes Disk identifier: 0x === top -i showed all 8 instances fo the parallel procedure md6_resync (CPU% 6) md5_resync (CPU% 0) kjournald After some time md6_resync, md5_resync, kjournald disappeared, leaving only the 8 parallel procedures. Commanding cat density6.out the parallel procedure seems to work regularly, confirmed by la -l which shows all files (some as large as 100MB) for the present computation
Re: Disk /dev/md6 doesn't contain valid partition table
In addition, cat /etc/fstab: # /etc/fstab: static file system information. # # file system mount point type options dump pass proc/proc procdefaults0 0 /dev/md2/ ext3defaults,errors=remount-ro 0 1 /dev/md0/boot ext3defaults0 2 /dev/md6/home ext3defaults0 2 /dev/md5/tmpext3defaults0 2 /dev/md3/usrext3defaults0 2 /dev/md4/varext3defaults0 2 /dev/md1noneswapsw 0 0 /dev/hda/media/cdrom0 udf,iso9660 user,noauto 0 0 /dev/fd0/media/floppy0 autorw,user,noauto 0 0 = file system ext3 = FilesystemSize Used Avail Use% Mounted on /dev/md2 14G 1.4G 12G 11% / tmpfs 12G 0 12G 0% /lib/init/rw udev 10M 128K 9.9M 2% /dev tmpfs 12G 0 12G 0% /dev/shm /dev/md0 2.8G 103M 2.6G 4% /boot /dev/md6 97G 1.1G 91G 2% /home /dev/md5 1.8G 33M 1.7G 2% /tmp /dev/md3 14G 6.6G 6.6G 50% /usr == What I am unable to documante from commands, is the presence of directory /opt where a non-GNU compiler and its math libraries are installed. The root directory reads: bin boot cdrom dev emul etc home initrd initrd.img initrd.img.old lib lib32 lib64 lost+found media mnt opt proc root sbin opt proc root sbin selinux srv sys tmp usr var vmlinuz vmlinuz.old == /dev/md4 2.8G 1.6G 1.1G 59% /var On Wed, Oct 29, 2008 at 8:24 AM, Francesco Pietra [EMAIL PROTECTED] wrote: On Wed, Oct 29, 2008 at 7:06 AM, Douglas A. Tutty [EMAIL PROTECTED] wrote: On Wed, Oct 29, 2008 at 05:44:31AM +0100, Francesco Pietra wrote: Major mistake (shutting down the ups unit) while doing a parallel computation on all 8 processors (UMA-type machine amd64 lenny with raid 1 two disks). On restarting the machine and the computation, fdisk -l showed Disk /dev/md6 doesn't contain a valid partition table df -h showed 97G 1.1G 91G 2% /home (which should have been ca 70% used). All other partitions were OK, as they should be. It would help us to follow if you provided a map of device to mount-point since, e.g. whe don't know what device is /home. As from my raid1 setup documantation: md 6 is /home/francesco/ md5 is /tmp Any command to check the above from the present status? In present status; cat /proc/mdstat: Personalities : [raid1] md6 : active raid1 sda8[0] sdb8[1] 102341952 blocks [2/2] [UU] md5 : active raid1 sda7[0] sdb7[1] 1951744 blocks [2/2] [UU] md4 : active raid1 sda6[0] sdb6[1] 2931712 blocks [2/2] [UU] md3 : active raid1 sda5[0] sdb5[1] 14651136 blocks [2/2] [UU] md1 : active(auto-read-only) raid1 sda2[0] sdb2[1] 6835584 blocks [2/2] [UU] md0 : active raid1 sda1[0] sdb1[1] 2931712 blocks [2/2] [UU] md2 : active raid1 sda3[0] sdb3[1] 14651200 blocks [2/2] [UU] unused devices: none = fdisk -l: Disk /dev/sda: 150.0 GB, 150039945216 bytes 255 heads, 63 sectors/track, 18241 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Disk identifier: 0x0009e776 Device Boot Start End Blocks Id System /dev/sda1 * 1 365 2931831 fd Linux raid autodetect /dev/sda2 3661216 6835657+ fd Linux raid autodetect /dev/sda31217304014651280 fd Linux raid autodetect /dev/sda43041 18213 121877122+ 5 Extended /dev/sda53041486414651248+ fd Linux raid autodetect /dev/sda648655229 2931831 fd Linux raid autodetect /dev/sda752305472 1951866 fd Linux raid autodetect /dev/sda85473 18213 102342051 fd Linux raid autodetect Disk /dev/sdb: 150.0 GB, 150039945216 bytes 255 heads, 63 sectors/track, 18241 cylinders Units = cylinders of 16065 * 512 = 8225280 bytes Disk identifier: 0x000b05ba Device BootDisk /dev/md2 doesn't contain a valid partition table Disk /dev/md0 doesn't contain a valid partition table Start End Blocks Id System /dev/sdb1 * 1 365 2931831 fd Linux raid autodetect /dev/sdb2 3661216 6835657+ fd Linux raid autodetect /dev/sdb31217304014651280 fd Linux raid autodetect /dev/sdb43041 18213 121877122+ 5 Extended /dev/sdb53041486414651248+ fd Linux raid autodetect /dev/sdb648655229 2931831 fd Linux raid autodetect /dev/sdb752305472 1951866 fd Linux raid autodetect /dev/sdb8
Re: Disk /dev/md6 doesn't contain valid partition table
On Wed, Oct 29, 2008 at 11:40 AM, Alex Samad [EMAIL PROTECTED] wrote: On Wed, Oct 29, 2008 at 08:24:55AM +0100, Francesco Pietra wrote: On Wed, Oct 29, 2008 at 7:06 AM, Douglas A. Tutty [EMAIL PROTECTED] wrote: On Wed, Oct 29, 2008 at 05:44:31AM +0100, Francesco Pietra wrote: [snip] cat /proc/mdstat: Personalities : [raid1] md6 : active raid1 sda8[0] sdb8[1] 102341952 blocks [2/2] [UU] md5 : active raid1 sda7[0] sdb7[1] 1951744 blocks [2/2] [UU] md4 : active raid1 sda6[0] sdb6[1] 2931712 blocks [2/2] [UU] md3 : active raid1 sda5[0] sdb5[1] 14651136 blocks [2/2] [UU] md1 : active(auto-read-only) raid1 sda2[0] sdb2[1] 6835584 blocks [2/2] [UU] md0 : active raid1 sda1[0] sdb1[1] 2931712 blocks [2/2] [UU] md2 : active raid1 sda3[0] sdb3[1] 14651200 blocks [2/2] [UU] This is off topic but, just a comment, it might be better instead of having lots of md's to have a big md raid1 and then sit lvm on top of it I am no system maintainer. I set up a raid1 according to the installation notes on Debian, I believe. At any event, this is the present situation. I must confess that a raid1 becomes dirty on power failure, although I expected that it works on one disk failure (as it happened to me once). Well, what about the following recipe that I found on internet? Could that be applied in my case as described? Thenks, francesco: 1. shutdown all processes and databases using the array. lsof /dev/md0 is your friend. 2. Full backup, in addition to the usual nightly ones. 3. Stop the array mdadm -S /dev/md0 4. Added the drive back into the array. In this case, mdadm /dev/md0 --add /dev/sdb1 5. Sit back and watch progress, watch -n 1 cat /proc/mdstat 6. Restart, dmesg says raid1: device sdc1 operational as mirror 1 raid1: device sdb1 operational as mirror 0 raid1: raid set md0 active with 2 out of 2 mirrors md: ... autorun DONE. [snip] Thanks francesco If so, you can write it back. Doug. -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] -- I'm thrilled to be here in the bread basket of America because it gives me a chance to remind our fellow citizens that we have an advantage here in America -- we can feed ourselves. - George W. Bush 08/23/2002 Stockton, CA -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iEYEARECAAYFAkkIPboACgkQkZz88chpJ2PBFQCgl4+OK7ZIigakH0NEA1xUlDtp qq8AoIqn0gS9axLCOZ03OoZ1w5qYSuIL =Oa83 -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Disk /dev/md6 doesn't contain valid partition table
Hi: Major mistake (shutting down the ups unit) while doing a parallel computation on all 8 processors (UMA-type machine amd64 lenny with raid 1 two disks). On restarting the machine and the computation, fdisk -l showed Disk /dev/md6 doesn't contain a valid partition table df -h showed 97G 1.1G 91G 2% /home (which should have been ca 70% used). All other partitions were OK, as they should be. top -i showed all 8 instances fo the parallel procedure md6_resync (CPU% 6) md5_resync (CPU% 0) kjournald After some time md6_resync, md5_resync, kjournald disappeared, leaving only the 8 parallel procedures. Commanding cat density6.out the parallel procedure seems to work regularly, confirmed by la -l which shows all files (some as large as 100MB) for the present computation and the 5 analogous computations already carried out (of these five computations I had scp sent a copy to my desktop). Where are the data for the current 6th computation being stored? The computer was then shutdown and restarted df -h output as above. fdisk -l Neither /dev/md6 nor /dev/md5 have a valid partition table. cd to my home shows all directories and files for work (in my home only data from computations, all applications installed in /usr/local). What could I do to set up the sytem in order before resuming the computation? Thanks francesco pietra -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Fw: Re: wine problems?
Frustrated by lack of functionality of installed package wine since I upgraded to i386 lenny, I purged removed all specific packages of wine and reinstalled, also my database application. Still hanging while commanding 'search'. Then I planned a more drastink purging. I first commanded apt-get --purge remove wine Then I explored what will happen from command apt-get --purge remove wine* The output screen from this command is shown below. Clearly I did not continue as it will remove gnome parts, in particular gnome-session, which is what I use after startx. Any suggestion? Thanks francesco pietra Reading package lists... Building dependency tree... Reading state information... Note, selecting libwine-capi for regex 'wine*' Note, selecting libchewing-data for regex 'wine*' Note, selecting libchewing3-data instead of libchewing-data Note, selecting libswing-layout-java for regex 'wine*' Note, selecting matchbox-window-manager for regex 'wine*' Note, selecting libwine-alsa for regex 'wine*' Note, selecting windows-el for regex 'wine*' Note, selecting plplot9-driver-xwin for regex 'wine*' Note, selecting libmono-winforms1.0-cil for regex 'wine*' Note, selecting libchewing3-data for regex 'wine*' Note, selecting wxwin-i18n for regex 'wine*' Note, selecting xwatchwin for regex 'wine*' Note, selecting libwine-twain for regex 'wine*' Note, selecting fte-xwindow for regex 'wine*' Note, selecting kwin-style-comix for regex 'wine*' Note, selecting kwin for regex 'wine*' Note, selecting xwininfo for regex 'wine*' Note, selecting wings3d for regex 'wine*' Note, selecting x-window-system-core for regex 'wine*' Note, selecting kwin-decor-baghira for regex 'wine*' Note, selecting avifile-win32-plugin for regex 'wine*' Note, selecting freepwing for regex 'wine*' Note, selecting x-window-system for regex 'wine*' Note, selecting cpio-win32 for regex 'wine*' Note, selecting libchewing-dev for regex 'wine*' Note, selecting scim-chewing for regex 'wine*' Note, selecting windowlab for regex 'wine*' Note, selecting libchewing2-dev for regex 'wine*' Note, selecting kwin-style-suse2 for regex 'wine*' Note, selecting winkeydaemon for regex 'wine*' Note, selecting libconfigwin-ocaml-dev for regex 'wine*' Note, selecting libcameleon-ocaml-dev instead of libconfigwin-ocaml-dev Note, selecting wine-utils for regex 'wine*' Note, selecting libchewing for regex 'wine*' Note, selecting libchewing3 instead of libchewing Note, selecting kwin-style-knifty for regex 'wine*' Note, selecting not+darwin for regex 'wine*' Note, selecting type-handling instead of not+darwin Note, selecting wininfo for regex 'wine*' Note, selecting worldwind for regex 'wine*' Note, selecting libwine-jack for regex 'wine*' Note, selecting hwinfo for regex 'wine*' Note, selecting grubutil-win32 for regex 'wine*' Note, selecting libchewing3 for regex 'wine*' Note, selecting wxwin2.4-headers for regex 'wine*' Note, selecting kwin-style-crystal for regex 'wine*' Note, selecting libmono-winforms2.0-cil for regex 'wine*' Note, selecting x-window-manager for regex 'wine*' Note, selecting libchewing3-dev for regex 'wine*' Note, selecting libwine for regex 'wine*' Note, selecting kwin4 for regex 'wine*' Note, selecting kwin-style-baghira for regex 'wine*' Note, selecting libwine-ldap for regex 'wine*' Note, selecting wine-bin for regex 'wine*' Note, selecting avant-window-navigator for regex 'wine*' Note, selecting wine-doc for regex 'wine*' Note, selecting libwine-gphoto2 for regex 'wine*' Note, selecting avant-window-navigator-data for regex 'wine*' Note, selecting twinkle for regex 'wine*' Note, selecting gzip-win32 for regex 'wine*' Note, selecting not+bsd-darwin for regex 'wine*' Note, selecting type-handling instead of not+bsd-darwin Note, selecting libwings-dev for regex 'wine*' Note, selecting wine for regex 'wine*' Note, selecting wing for regex 'wine*' Note, selecting wink for regex 'wine*' Note, selecting libwine-print for regex 'wine*' Note, selecting kwin-style-dekorator for regex 'wine*' Note, selecting openwince-jtag for regex 'wine*' Note, selecting libgnome-window-settings1 for regex 'wine*' Note, selecting kdeartwork-theme-window for regex 'wine*' Note, selecting libwine-dbg for regex 'wine*' Note, selecting libwine-dev for regex 'wine*' Note, selecting libwine-cms for regex 'wine*' Note, selecting libwine-gl for regex 'wine*' Note, selecting worldwind-doc for regex 'wine*' Note, selecting libwine-esd for regex 'wine*' Note, selecting libgnome-window-settings-dev for regex 'wine*' Note, selecting wing-data for regex 'wine*' Note, selecting libworldwind-java for regex 'wine*' Note, selecting kwin-style-powder for regex 'wine*' Note, selecting libswingx-java for regex 'wine*' Note, selecting libwine-nas for regex 'wine*' Note, selecting winbind for regex 'wine*' Note, selecting libwine-oss for regex 'wine*' Note, selecting winpdb for regex 'wine*' Note, selecting libswing-layout-java-doc for regex 'wine*' Note, selecting openwince-include for regex 'wine
Re: Fw: Re: wine problems?
Thanks. I followed the right recipe and the carried out a fresh install of wine. Everything shows a correct installation, like dpkg --status wine The windows application (a database) installs, though it fails to work. Like before. I have already abandoned the windows application chemsk50 as chem drawing package as there is now gchampaint. Hope to find a linux alternative to the free-form database. francesco On Sun, Jun 8, 2008 at 8:03 PM, Florian Kulzer [EMAIL PROTECTED] wrote: On Sun, Jun 08, 2008 at 19:31:06 +0200, Francesco Pietra wrote: Frustrated by lack of functionality of installed package wine since I upgraded to i386 lenny, I purged removed all specific packages of wine and reinstalled, also my database application. Still hanging while commanding 'search'. Then I planned a more drastink purging. I first commanded apt-get --purge remove wine Then I explored what will happen from command apt-get --purge remove wine* The output screen from this command is shown below. Clearly I did not continue as it will remove gnome parts, in particular gnome-session, which is what I use after startx. Any suggestion? Reading package lists... Building dependency tree... Reading state information... Note, selecting libwine-capi for regex 'wine*' Note, selecting libchewing-data for regex 'wine*' Note, selecting libchewing3-data instead of libchewing-data Note, selecting libswing-layout-java for regex 'wine*' [...] For apt-get the regular expression 'wine*' will match any package whose name contains the string win. You are mixing up shell globbing patterns and regular expressions; see man 7 regex for the correct regex syntax. (Moreover, things can get really messy if you have any files in the current directory whose names start with wine; see the section Pathname Expansion in the manpage of bash.) Try apt-get -s --purge remove 'wine.*' and if this shows the right output then you can run the same command without the -s to actually remove and purge these packages. (Note: I have no idea if puring and reinstalling all those wine packages will solve your original problem.) -- Regards,| http://users.icfo.es/Florian.Kulzer Florian | -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] -- Dr Francesco Pietra Professor of Chemistry Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594 Palazzo Ducale 55100 Lucca (Italy) -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug with package 'wine' ?
Applications driven by wine 1.0-rc1-1 (which 'dpkg --status wine' seems to be correctly installed) either do not start any more, or they start but lack functionalities and hang. Example of the latter: [EMAIL PROTECTED]:~$ /home/francesco/.wine/drive_c/Program Files/programY.exe fixme:msvcrt:__lconv_init stub fixme:shdocvw:PersistStreamInit_InitNew (0x16f2c0) err:ole:ITypeInfo_fnInvoke did not find member id -518, flags 0x4! err:ole:ITypeInfo_fnInvoke did not find member id -517, flags 0x4! fixme:shdocvw:OleInPlaceObject_InPlaceDeactivate (0x16f2c0) fixme:shdocvw:OleObject_Close (0x16f2c0)-(1) fixme:win:LockWindowUpdate (0x3014a), partial stub! fixme:win:LockWindowUpdate ((nil)), partial stub! ___- Example of application that does not start: [EMAIL PROTECTED]:~$ /home/francesco/.wine/drive_c/ACDFREE5/CHEMSK.EXE fixme:ole:CoResumeClassObjects stub [EMAIL PROTECTED]:~$ francesco pietra -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
wine problems?
After having upgraded to lenny i386, the two applications I used with wine have problems. One (a chemical drawing package) does not start any more. The other one (a database) starts, though functionalities are greatly reduced and it hangs quite easily. Am alone having such problems? Do they depend from the wine version currently on i386 or from the deb packaging? I have purged-removed all wine and reinstalled; same problems. Thanks francesco pietra -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: libsc7_2.3.1-3_amd64.deb problems
Hi: #apt-get --purge remove libsc8 libsc-doc libsc-dev libsc7 completed by synaptic removal of libsc-doc (which was not removed by the above command) followed by #apt-get update #apt-get upgrade now only reports errors exim4-daemon-ligth at exim4 bsd-mailx acpid mailx which (as from Floria Kulzer) seems be bug #477258, which has been fixed in Sid since April 25, exim4 version 4.69-3. The bug report describes how to repair the init script yourself. (So far the fix did not propagate to Lenny because there have been further updates in Sid, restarting the 10 days waiting period.) I do nothing more if, as I expect, apt-get upgrade will do the repair in due time. Why these errors did not show up of amd64 when the system complained about libsc7 is something I do not understand. I got the impression that the libsc7 deb package is faulty. Thanks francesco --- On Tue, 5/6/08, Lennart Sorensen [EMAIL PROTECTED] wrote: From: Lennart Sorensen [EMAIL PROTECTED] Subject: Re: libsc7_2.3.1-3_amd64.deb problems To: Francesco Pietra [EMAIL PROTECTED] Cc: C. Ahlstrom [EMAIL PROTECTED], debian64 [EMAIL PROTECTED], debian-users debian-user@lists.debian.org Date: Tuesday, May 6, 2008, 11:37 AM On Tue, May 06, 2008 at 11:33:54AM -0700, Francesco Pietra wrote: I have tried with synaptic. (1) marking libsc8 (which was installed) for removal and unmarking libsc7_2.3.1-3_amd64.deb (which was not installed), a dist-upgrade is carried out, ending in the same error: E: /var/cache/apt/archives/libsc7_2.3.1-3_amd64.deb trying to overwrite '/usr/lib/libSCstates.so.7.1.0' whi is also in package libsc8. Now marking libsc-dev for removal returns errors: E: exim-daemon-light subprocesses post-installation script returned error exit status 1 E: exim4 depend problem E: bds-mailx dep problem E: acpid subprocess post-install error 1 E: mailx dep problem I.e, it drops now in the same errors that I had reported for i386. Florian Kulzer [EMAIL PROTECTED] kindly advided me that it is a bug fixed in unstable, not yet passed to lenny. Try doing: dpkg --purge libsc8 apt-get install libsc7 If the dpkg fails, then something must still be using it. -- Len Sorensen -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Fw: Errors on upgrading from etch to lenny
Hi: I wonder whether the debian-user list is still active. When posting for help at the amd64 list, even from inexperienced users, the amd64 list usually provides help overnight. See please my request for help below to the debian-users list. Unanswered. Notice, please, that no such errors came out when upgrading from etch to lenny with amd64. Of course I understand that a general list such as debian-users may be very crowded. Therefore, this is just a respectfully remind. Must add that I tried all obvious resources to resolve the issue, such as apt-get -f install and others, without success. Thanks francesco pietra --- On Sat, 5/3/08, Francesco Pietra [EMAIL PROTECTED] wrote: From: Francesco Pietra [EMAIL PROTECTED] Subject: Errors on upgrading from etch to lenny To: debian-users debian-user@lists.debian.org Date: Saturday, May 3, 2008, 10:28 AM May I ask how to resolve errors (sub-process /usr/bin/dpkg returned error code 1) about exim4-daemon-light at exim4 bsd-mailx mailx as the result of upgrading i386 from etch to lenny. Can't find which program is affected (mail from gnome, ssh, in situ compiled graphic programs, programs driven by wine, all OK). Thanks francesco pietra Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Fw: Errors on upgrading from etch to lenny
Hi: The full error message is: deb32:/home/francesco# apt-get install -f Reading package lists... Done Building dependency tree... Done 0 upgraded, 0 newly installed, 0 to remove and 53 not upgraded. 5 not fully installed or removed. After this operation, 0B of additional disk space will be used. Setting up exim4-daemon-light (4.69-2+b1) ... Starting MTA:exim: incompatible command-line options or arguments invoke-rc.d: initscript exim4, action start failed. dpkg: error processing exim4-daemon-light (--configure): subprocess post-installation script returned error exit status 1 dpkg: dependency problems prevent configuration of at: at depends on mail-transport-agent; however: Package mail-transport-agent is not installed. Package exim4-daemon-light which provides mail-transport-agent is not configured yet. dpkg: error processing at (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of exim4: exim4 depends on exim4-daemon-light | exim4-daemon-heavy | exim4-daemon-custom; however: Package exim4-daemon-light is not configured yet. Package exim4-daemon-heavy is not installed. Package exim4-daemon-custom is not installed. dpkg: error processing exim4 (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of bsd-mailx: bsd-mailx depends on exim4 | mail-transport-agent; however: Package exim4 is not configured yet. Package mail-transport-agent is not installed. Package exim4-daemon-light which provides mail-transport-agent is not configured yet. dpkg: error processing bsd-mailx (--configure): dependency problems - leaving unconfigured dpkg: dependency problems prevent configuration of mailx: mailx depends on bsd-mailx; however: Package bsd-mailx is not configured yet. dpkg: error processing mailx (--configure): dependency problems - leaving unconfigured Errors were encountered while processing: exim4-daemon-light at exim4 bsd-mailx mailx E: Sub-process /usr/bin/dpkg returned an error code (1) Thanks francesco pietra --- On Tue, 5/6/08, Florian Kulzer [EMAIL PROTECTED] wrote: From: Florian Kulzer [EMAIL PROTECTED] Subject: Re: Fw: Errors on upgrading from etch to lenny To: debian-user@lists.debian.org Cc: [EMAIL PROTECTED] Date: Tuesday, May 6, 2008, 1:13 AM On Tue, May 06, 2008 at 00:08:35 -0700, Francesco Pietra wrote: Hi: I wonder whether the debian-user list is still active. When posting for help at the amd64 list, even from inexperienced users, the amd64 list usually provides help overnight. See please my request for help below to the debian-users list. Unanswered. Your original message (17:28:33 UTC): http://lists.debian.org/debian-user/2008/05/msg00201.html An answer (18:07:33 UTC): http://lists.debian.org/debian-user/2008/05/msg00204.html Maybe you missed the answer because you expected to get a CC to your own email address and therefore you did not follow the list closely enough. The fact that your messages have a Reply-To header pointing to your own email address does not mean that you will automatically be CC'd if somebody replies to the list. You have to explicitly ask to be CC'd or you have to include an appropriate Mail-Followup-To header. I am CC'ing you now to make sure that you get this message, even though this is technically a violation of the list policy. I assume this is what you wanted, since I cannot otherwise see the point of generating a Reply-To header that is identical to the From address. Notice, please, that no such errors came out when upgrading from etch to lenny with amd64. Of course I understand that a general list such as debian-users may be very crowded. Therefore, this is just a respectfully remind. Must add that I tried all obvious resources to resolve the issue, such as apt-get -f install and others, without success. It seems be bug #477258, which has been fixed in Sid since April 25, exim4 version 4.69-3. The bug report describes how to repair the init script yourself. (So far the fix did not propagate to Lenny because there have been further updates in Sid, restarting the 10 days waiting period.) -- Regards,| http://users.icfo.es/Florian.Kulzer Florian | Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: libsc7_2.3.1-3_amd64.deb problems
I have tried with synaptic. (1) marking libsc8 (which was installed) for removal and unmarking libsc7_2.3.1-3_amd64.deb (which was not installed), a dist-upgrade is carried out, ending in the same error: E: /var/cache/apt/archives/libsc7_2.3.1-3_amd64.deb trying to overwrite '/usr/lib/libSCstates.so.7.1.0' whi is also in package libsc8. Now marking libsc-dev for removal returns errors: E: exim-daemon-light subprocesses post-installation script returned error exit status 1 E: exim4 depend problem E: bds-mailx dep problem E: acpid subprocess post-install error 1 E: mailx dep problem I.e, it drops now in the same errors that I had reported for i386. Florian Kulzer [EMAIL PROTECTED] kindly advided me that it is a bug fixed in unstable, not yet passed to lenny. francesco --- On Tue, 5/6/08, Lennart Sorensen [EMAIL PROTECTED] wrote: From: Lennart Sorensen [EMAIL PROTECTED] Subject: Re: libsc7_2.3.1-3_amd64.deb problems To: Francesco Pietra [EMAIL PROTECTED] Cc: C. Ahlstrom [EMAIL PROTECTED], debian64 [EMAIL PROTECTED] Date: Tuesday, May 6, 2008, 9:32 AM On Tue, May 06, 2008 at 08:53:27AM -0700, Francesco Pietra wrote: Hi: Sorry for this lengthy dealing with libsc7/libsc8, though I would like to clean the system, i.e. not to have these issues raised at each apt-get upgrade. Actually, now apt-get upgrade only results in: Reading package list ...Done Building dependency tree ... Done You might want to run 'apt-get -f install' to correct. Packages with unmet dependencies: libsc-dev: Depends: libsc7 (= 2.3.1-3) but it is not installed. It seems to be unable to upgrading, unless there is nothing else. I think that I don't need either libsc7 or libsc8. Both come from The Scientific Computing Toolkit (Sandja Lab, mpqc) an extraordinary quantum mechanical package that I used successfully, but one that unfortunately is not being developed toward organic chemical applications. Therefore I don't use it any more. There is a relationship with ghemical that I don't use either on this amd64 system (I barely run 'startx' on rare occasions) I did some search: apt-cache rdepends libsc7 ENTER Reverse Depends: mpqc-support mpqc libsc-dev libghemical3gf apt-cache rdepends libsc8 ENTER Reverse Depends: [nothing reported] If I carry out the same commands with i386 (where mpqc is still installed), for libsc7 there is one line more libghemical0c2a, while for libsc8 the answer is no package found. Well mpqc seems to use it too. It seems odd that libsc8 conflicts with libsc7, in fact I would think that is a bug and should be reported as such. If nothing else it should conflict if it can't be installed at the same time. -- Len Sorensen -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Errors on upgrading from etch to lenny
May I ask how to resolve errors (sub-process /usr/bin/dpkg returned error code 1) about exim4-daemon-light at exim4 bsd-mailx mailx as the result of upgrading i386 from etch to lenny. Can't find which program is affected (mail from gnome, ssh, in situ compiled graphic programs, programs driven by wine, all OK). Thanks francesco pietra Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Fwd: Total vs per-cpu memory
Sorry for the mistake, although otherwise clear from the context: 16GB total is correct as there are 4GB per cpu. francesco --- Francesco Pietra [EMAIL PROTECTED] wrote: Date: Thu, 31 Jan 2008 07:39:43 -0800 (PST) From: Francesco Pietra [EMAIL PROTECTED] Subject: Total vs per-cpu memory To: debian64 [EMAIL PROTECTED] This question is related to problems in running a docking computation. With big cases, RAM proves insufficient, resulting in immediate segmentation fault, so that top cannot inform. Though, from the code it is clear that memory is insufficient to rotate the object in a non-parallelized part of the program. Smaller objects do not give problems. My question is: with Tyan S2895 Thunder K8WE, two dual opterons and 1GB RAM per cpu (amd64 etch), are the 16GB available to the single cpu involved in the computation, or are 4GB available? Memory was set with shmmax: kernel.shmmax = 160 kernel.shmall = 160 sysctl -p Thanks francesco pietra Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Env var on the fly
Having defined (in my .bashrc) the environmental variables for computing suites X and Y (PATH to them) it happens - because of some bug in X - that on running certain programs of Y, executables of X are called (and of course not found). If I undefine the env var X, all programs of Y run perfectly. Is any simple way to define the env var X on the fly, when X is needed, without having to use X as another user? (which would overcomplicate the matter because there is an scp link from the computing machine to and from a desktop, where I am). debian linux amd64 etch on the computing machine, where my .bashrc. deain linux i386 etch on the desktop. Thanks francesco pietra Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
double raid 1 filesystem
I need more fast-HD space for computational work. I wonder whether by adding a second SATA raid1 (a couple of new disks) to the existing SATA raid1, my home could be spread on the two raid1 systems, as if it were a single disk (or filesystem, if you want). At the moment, on the Tyan S2895 Thunder K8WE, with OS Debian amd64 etch, there is a raid1 arrangement made with two WD Raptor 150GB each. That affords 100GB free space for collecting data. If I had to rely solely on the 150BG of a second, new, raid1, space would be insufficient. I need to have 100 + 150GB. Raptor HDs exist at 150GB max size. On the other hand, 300GB Maxtor initially installed proved to be incompatible with the board components, resulting, from time to time, in memory corruption. Disks were reconstructed by the raid1, though the job was lost. In those instances jobs were already running since ca one month. Thanks francesco pietra Need a vacation? Get great deals to amazing places on Yahoo! Travel. http://travel.yahoo.com/ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Script polluted by DOS formatting
A script downloaded to a desktop i386/etch/gnome from Amber web site, edited on the desktop with gnome text editor, then sent scp to a computing machine amd64, turned out to be polluted by DOS formatting. The computing program was prevented from reading the polluted lines. I tried dos2unix scriptfilename which failed to clean the script. Opening the script with vim did not reveal the problem. It was only od -c scriptfilename od.dmp that revealed non printing characters, octal 302 followed by octal 240 at each script line. I was unfamiliar with such affairs and wonder about the origin of the pollution. The desktop has wine installed (for a Windows-based database that finds no efficient substitute in unix) and may be (don't remember) the database had been launched before editing of the said script. 1) Is wine likely to have caused the pollution? 2) Is the above dos2unix command correctly issued? Thanks francesco pietra Building a website is a piece of cake. Yahoo! Small Business gives you all the tools to get online. http://smallbusiness.yahoo.com/webhosting -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Header files amd64 etch
A mixed compilation (ifort/gcc 4.1.2) of Amber9 on amd64 etch dual-core-opterons (Linux deb32 2.6.18-3-k7 #1 SMP Mon Dec 4 17:23:11 UTC 2006 i686 GNU/Linux) requests the following header files; WcActCB.c:22:28: error: X11/IntrinsicP.h: No such file or directory WcActCB.c:29:24: error: X11/ShellP.h: No such file or directory as the single errors out of an enormous number of modules that passed make. As a beginner in compilations, I would appreciate being instructed how to find the appropriate (64bit if they differ from 32bit) headers. I have seen packages that provide all headers, though above etch, with a more recent kernel. In other words, I don't know the appropriate console command to trace the package to install. And, for the moment I refrain from dist upgrade. Thanks francesco pietra Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Fwd: Header files amd64 etch
Probably I have found the way with apt-cache search (show) xorg-dev V 1:7.1.0-16 fp --- Francesco Pietra [EMAIL PROTECTED] wrote: Date: Fri, 29 Jun 2007 23:00:52 -0700 (PDT) From: Francesco Pietra [EMAIL PROTECTED] Subject: Header files amd64 etch To: debian-users debian-user@lists.debian.org, debian64 [EMAIL PROTECTED] A mixed compilation (ifort/gcc 4.1.2) of Amber9 on amd64 etch dual-core-opterons (Linux deb32 2.6.18-3-k7 #1 SMP Mon Dec 4 17:23:11 UTC 2006 i686 GNU/Linux) requests the following header files; WcActCB.c:22:28: error: X11/IntrinsicP.h: No such file or directory WcActCB.c:29:24: error: X11/ShellP.h: No such file or directory as the single errors out of an enormous number of modules that passed make. As a beginner in compilations, I would appreciate being instructed how to find the appropriate (64bit if they differ from 32bit) headers. I have seen packages that provide all headers, though above etch, with a more recent kernel. In other words, I don't know the appropriate console command to trace the package to install. And, for the moment I refrain from dist upgrade. Thanks francesco pietra Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center. http://autos.yahoo.com/green_center/ -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Re: Fwd: Header files amd64 etch
Marko: Thanks. The installation of xorg-dev includes libxt-dev. Though, make failed again. I have been instructed to first carry out a serial installation, and parallel only after serial is OK. If not else because parallel does not compile all modules. However, the configure command line ./configure -static ifort_x86_64 implies that gcc is taken from the system. If I understand, gcc is not prepared to furnish static libraries (not checked). Why things are not set up for a homogeneous compilation (intel provides *.a libraries) is not clear to me. The parallel compilation will be homogenous, with intels for fortran, C and C++ for bothe amber and openmpi. Cheers francesco --- Marko Randjelovic [EMAIL PROTECTED] wrote: Francesco Pietra wrote: Probably I have found the way with apt-cache search (show) xorg-dev V 1:7.1.0-16 fp I don't think so. Try this: [EMAIL PROTECTED]:~$ apt-file search X11/IntrinsicP.h libxt-dev: usr/include/X11/IntrinsicP.h [EMAIL PROTECTED]:~$ apt-file search X11/ShellP.h libxt-dev: usr/include/X11/ShellP.h So, you need package libxt-dev. -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED] 8:00? 8:25? 8:40? Find a flick in no time with the Yahoo! Search movie showtime shortcut. http://tools.search.yahoo.com/shortcuts/#news -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
