[gmx-users] installation error under openSuse 12.2
Date: Mon, 11 Nov 2013 08:27:05 -0800 (PST) From: kolnkempff kolnkem...@gmail.com Subject: [gmx-users] installation error under openSuse 12.2 To: gmx-users@gromacs.org Message-ID: 1384187225465-5012430.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Dear gmx-users, I am trying to install gromacs-4.6.3 on an older Dell that is running openSuse 12.2 Using DGMX_BUILD_OWN_FFTW=ON failed for me so to get through cmake I had to compile fftw from scratch and I followed the recommendation of going directly to their website. Now I am at the make stage and get the following message: [ 67%] Built target gmxfftw make[2]: *** No rule to make target `//home/koln/bin/gromacs-4.6.3/build/src/contrib/fftw/gmxfftw-prefix/lib/libfftw3f.a', needed by `src/gmxlib/libgmx.so.8'. Stop. make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2 make: *** [all] Error 2 When I check for libfftw, I get: koln@linux-5bim:~/bin/gromacs-4.6.3/build2 rpm -qf /usr/lib/libfftw3f.* libfftw3-3-32bit-3.3.2-1.1.2.x86_64 Any suggestions for how to get past this obstacle would be greatly appreciated! This is an known issue in OpenSuse! We added a workaround a while ago: https://gerrit.gromacs.org/#/c/2540/ Until Gromacs release 4.6.4. you will have to change line 41 of src/contrib/fftw/CMakeLists.txt yourself or just install fftw through OpenSuse or by hand. Christoph Koln -- View this message in context: http://gromacs.5086.x6.nabble.com/installation-error-under-openSuse-12-2-tp5012430.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: 'Command not found' after installation
Date: Sun, 25 Aug 2013 14:31:51 -0700 (PDT)
From: Nimmy McNimmerson nimzs...@yahoo.com
Subject: Re: [gmx-users] 'Command not found' after installation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
1377466311.57911.yahoomail...@web122305.mail.ne1.yahoo.com
Content-Type: text/plain; charset=iso-8859-1
Hmm... To be honest I'm a novice at installing complex things, I'm a computer
scientist by trade but I'm not very good at troubleshooting this kind of
thing. Has anyone actually installed GROMACS on mac and what did you do?
(Using the default gcc/g++ doesn't work for the AVX stuff)
I got it working, but with gcc, only.
I would try the following:
1.) Find libiomp5.dylib
find / -iname libiomp5.dylib
2.) Update dyld search path by adding the directory from step 1
export DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:/path/to/libiomp5
to your .bashrc or GMXRC.bash
Christoph
From: Mark Abraham mark.j.abra...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Sunday, August 25, 2013 12:57 AM
Subject: Re: [gmx-users] 'Command not found' after installation
Hi,
I don't have any experience with icc on Mac, but I would try either
* re-reading the icc docs to see whether you should be source-ing some
configuration file to set up the dynamic loading at run time (as well
as at compile time), and/or
* making a static build (cmake -DBUILD_SHARED_LIBS=off; but some
Google hits suggests icc was broken at some point and iomp5 enforces
dynamic linking, go figure!),
* when you're really sure you've set up your build environment
correctly, complaining at Intel (again) :-)
Mark
On Sun, Aug 25, 2013 at 7:18 AM, Nimmy McNimmerson nimzs...@yahoo.com wrote:
Hi,
Apparently this is an issue with my intel compiler; the dynamic linker isn't
finding the libiomp5.dylib library. However, I don't know how to fix this
(the google results haven't worked.)
Please help,
Thanks,
John
From: Barnett, James W. jbarn...@tulane.edu
To: nimzs...@yahoo.com
Sent: Saturday, August 24, 2013 3:07 PM
Subject: Re: [gmx-users] 'Command not found' after installation
Unfortunately this is now beyond what I know with a Mac. It sounds like a
library is missing that GROMACS needs, or GROMACS can't find it, which is
probably a simple fix.
Perhaps someone more familiar with Mac will be able to weigh in.
jbarn...@tulane.edu | from mobile
nimzs...@yahoo.com wrote:
This gives the following:
dyld: Library not loaded: libiomp5.dylib
Referenced from: /usr/local/gromacs/bin/g_luck
Reason: image not found
Trace/BPT trap: 5
If I try 'pdb2gmx', it says:
dyld: Library not loaded: libiomp5.dylib
Referenced from: /usr/local/gromacs/bin/pdb2gmx
Reason: image not found
Trace/BPT trap: 5
Did the installation not work properly?
From: Barnett, James W. jbarn...@tulane.edu
To: Nimmy McNimmerson nimzs...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Saturday, August 24, 2013 10:42 AM
Subject: Re: [gmx-users] 'Command not found' after installation
Try g_luck. That's what has worked for me.
On 08/24/2013 12:37 PM, Nimmy McNimmerson wrote:
Hello all,
I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I
downloaded the latest Intel C++ compilers and built Gromacs successfully
(at least it appeared to be successful since I saw no error messages). I
appended this line to my ~/.profile file: source
/usr/local/gromacs/bin/GMXRC.bash, and restarted my terminal. Still, every
time I type in a GROMACS command, such as luck, it says command not
found. f I do echo $GMXDATA, it does return
/usr/local/gromacs/share/gromacs, though.
Thanks,
John
--
Wes Barnett | jbarn...@tulane.edu
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[gmx-users] Re: Unable to download Gromacs source tar file
Date: Sat, 8 Jun 2013 13:57:51 +0200 From: Mark Abraham mark.j.abra...@gmail.com Subject: Re: [gmx-users] Unable to download Gromacs source tar file To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: camnumasy_p5tqoarcvgat1qd0wb2dwfh9ouhvfk-83vauh8...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 As a work-around, you can try to get archives from https://github.com/gromacs/gromacs/tags (but these will not quite match the official tarballs - but in ways that don't matter for simulating). Or use google to find the tarball: https://www.google.com/search?q=intitle:%22index+of%22+gromacs-4.6.1.tar.gz Christoph Mark On Sat, Jun 8, 2013 at 1:54 PM, Mark Abraham mark.j.abra...@gmail.comwrote: I just downloaded the 4.5.7 tarball to a machine in Australia. Mark On Sat, Jun 8, 2013 at 1:23 PM, Chandan Choudhury iitd...@gmail.comwrote: I too cannot download (tried with 3.3 4.5.5 4.6 and 4.5.7). Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Jun 8, 2013 at 4:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote: They're still fine. There must be a problem at your end, I'm afraid. Mark On Sat, Jun 8, 2013 at 10:46 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, Thanks for your reply. But the problem still persists. Even now I am not able to download. -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham Sent: Fri 6/7/2013 8:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Unable to download Gromacs source tar file They're fine now. Perhaps the FTP server was offline briefly. Mark On Fri, Jun 7, 2013 at 7:41 AM, Bhamy Maithry Shenoy bhamymait...@aero.iisc.ernet.in wrote: Hi, I would like to use Gromacs for MD simulation of biomolecules. But I am not able to download any of the source files from the link http://www.gromacs.org/Downloads Can anyone please help. Thanks and regards, Maithry -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Langevin thermostat implementation in GROMACS vs AMBER
Date: Wed, 08 May 2013 16:34:46 +0200
From: Julian Garrec julian.gar...@epfl.ch
Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS
vs AMBER
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 518a6286.8020...@epfl.ch
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
No suggestion ?? :)
In my post I forgot to say that my system contains explicit water.
I'm still very curious about the difference in implementation in AMBER
and GROMACS. And I still don't really understand the meanning of tau-t
in LD and how it is related to other (well defined) quantities such as
the friction coeficient in equation 3.114 of the manual (v4.6.1).
I am not really sure what your question is, section 7.3.3 is pretty
clear about that:
the inverse friction constant for each group is set with tau-t, so
gamma_i=1/tau-t, which also makes sense unit-wise as gamma has units
1/ps and tau-t ps
bd-fric is only used for the Brownian dynamics integrator and if
bd-fric=0, the friction is calculated as mass/tau-t. It might be a bit
misleading that bd-fric is listed under section 7.3.4 (Langevin
dynamics), but that stems from the fact that Brownian dynamics is the
overdamped case of stochastic dynamics and hence it is Langevin
Dynamics, too, just in a different limit.
Christoph
Please help,
Sincerely,
Julian
Le 04/05/13 13:42, Julian Garrec a 閏rit :
Dear all,
I am trying to use stochastic dynamics in GROMACS to reproduce some
previous results that I got with the AMBER software using the Langevin
thermostat.
In AMBER, one typically sets what they call the collision frequency
(noted gamma_ln in the AMBER manual). I typically set gamma_ln to 2
collisions per ps (significantly smaller than the internal friction of
water, since I use Langevin dynamics as a thermostat).
1) In the mdp options manual, it is recommended to use {integrator=sd
; bd-fric=0 ; tau-t=2}. My understanding is that bd-fric corresponds
to 'm_i*gamma_i' in equation 3.114 of the theoretical part of the
manual (version 4.6.1). Am I right ?
2) Then, is {integrator=sd ; bd-fric=0 ; tau-t=2} equivalent to
{integrator=sd ; bd-fric=0.5} ? (In the theoretical part of the
manual, it is said that gamma_i should be set to 0.5 to follow the
same spirit).
3) Is 'bd-fric' of GROMACS equivalent to 'gamm_ln' of AMBER ?
Thanks for your help,
Julian
--
Julian Garrec, research associate
Web: https://sites.google.com/site/juliangarrec/
蓂uipe : Chimie et Biochimie Th閛riques
Unit�Mixte de Recherches CNRS UHP 7565
Universit�de Lorraine, Nancy I BP 239,
54506 Vandoeuvre-l鑣-Nancy, cedex France
--
Christoph Junghans
Web: http://www.compphys.de
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[gmx-users] Re: installation Gromacs-Fedora18
is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from cc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC checking if cc PIC flag -fPIC works... yes checking if cc static flag -static works... no checking if cc supports -c -o file.o... yes checking whether the cc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes configure: creating libtool appending configuration tag CXX to libtool checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC checking if g++ PIC flag -fPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate appending configuration tag F77 to libtool checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3... no configure: error: Cannot find fftw3 library Please can you advise me what should I do to solve this error thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Francesco frac...@myopera.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Manual installation of new analysis tool
'* *dist_mode.c:(.text+0x6a3): undefined reference to `save_calloc'* *dist_mode.c:(.text+0x710): undefined reference to `save_calloc'* *dist_mode.c:(.text+0x73f): undefined reference to `save_calloc'* *dist_mode.o:dist_mode.c:(.text+0x76e): more undefined references to `save_calloc' follow* *dist_mode.o: In function `build_dist':* *dist_mode.c:(.text+0x7b2): undefined reference to `get_index'* *dist_mode.c:(.text+0x839): undefined reference to `xvgropen'* *dist_mode.c:(.text+0x865): undefined reference to `xvgr_legend'* *dist_mode.o: In function `clean_dist':* *dist_mode.c:(.text+0x8bd): undefined reference to `save_free'* *dist_mode.c:(.text+0x8f1): undefined reference to `save_free'* *dist_mode.c:(.text+0x917): undefined reference to `save_free'* *dist_mode.c:(.text+0x948): undefined reference to `save_free'* *grid_mode.o: In function `build_grids':* *grid_mode.c:(.text+0x81): undefined reference to `save_calloc'* *grid_mode.c:(.text+0x177): undefined reference to `gmx_fatal'* *grid_mode.c:(.text+0x1a2): undefined reference to `save_calloc'* *grid_mode.c:(.text+0x201): undefined reference to `ffopen'* *grid_mode.o: In function `clean_grids':* *grid_mode.c:(.text+0x2b8): undefined reference to `save_free'* *grid_mode.c:(.text+0x2c6): undefined reference to `ffclose'* *grid_mode.c:(.text+0x2e9): undefined reference to `save_free'* *grid_mode.o: In function `grid_store':* *grid_mode.c:(.text+0x41a): undefined reference to `put_atom_in_box'* *collect2: ld returned 1 exit status* *make: *** [g_mydensity] Error 1* Please help me in this regard. Thanks for your valuable time and concern. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition
--prefix=/usr/users/iff_th2/**liao/gromacs454/ --enable-double --enable-threads CC=gcc --disable-gcc41-check --enable-mpi --program-suffix=_d 1056 make The error showed to me was: /usr/bin/ld: /usr/local/lib/libfftw3.a(**plan-dft-c2r-2d.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not read symbols: Bad value I added the option of --with-fPIC, but it was not recognized, and then I changed it to --with-pic, but the error was still the same. I don't know why gromacs can recognize the fftw library when doing the single float compilation, but not for the double float compilation, I already used the shared option. Could someone give me some suggestions to help me this out? Any reply will be appreciated. In your last step, you're not using --enable-shared like you did in every preceding step. Adding that flag should fix it. http://www.gromacs.org/**Documentation/Installation_** Instructions_4.5#Details_for_**building_the_FFTW_prerequisite http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite Gromacs 4.5.4 is pretty old; is there any reason you're not using a new version? You'll get much better performance from 4.6.1. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, Qinghua -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Best Regards, Qinghua -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 107, Issue 116 *** -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gromacs VERSION 4.0.7-There is no domain
Date: Sun, 10 Mar 2013 03:17:24 -0700 (PDT) From: Hamid Mosaddeghi hamid5920...@yahoo.com Subject: [gmx-users] Re: gromacs VERSION 4.0.7-There is no domain decomposition. To: gmx-users@gromacs.org Message-ID: 1362910644976-5006251.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Dear Christoph thanks for quick reply It seems like mdrun was not able to find a decomposition automatically, try to give one by hand: $ mdrun -dd 2 2 4 this command is general or not? No, it is not general, but you wanted to run on 16 cores, so a decomposition of 2x2x4 (=16 and 4 in z as the box was the longest in z) would work. Btw, your gromacs is 2 major versions behind, it might be a good idea to update yes, but I modify some force field in this versiom nad need to work with it If this change is of general interest, create a patch and submit it here: https://gerrit.gromacs.org/ do you think I go to new version, don't get this error? Many many things has been improved from 4.0 to 4.6, so I think it is save to say it will most likely work. Best Regards Hamid Mosaddeghi -- View this message in context: http://gromacs.5086.n6.nabble.com/Re-gromacs-VERSION-4-0-7-There-is-no-domain-decomposition-tp5006247p5006251.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 107, Issue 42 ** -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gromacs VERSION 4.0.7-There is no domain decomposition.....
Dear Hamid, please post these kind of questions on the users and not the developers list. 2013/3/9 Hamid Mosaddeghi hamid5920...@yahoo.com: Dear users I used gromacs for my system include CNT-water-ion-protein (400,000atom), I used grompp without error. after used mdrun with 16 node on cluster, I get this error: Reading file nvt.tpr, VERSION 4.0.7 (single precision) Loaded with Money NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off Will use 15 particle-particle and 1 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.0.7 Source code file: domdec.c, line: 5888 Fatal error: There is no domain decomposition for 15 nodes that is compatible with the given box and a minimum cell size of 3.75 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- Good Music Saves your Soul (Lemmy) Error on node 0, will try to stop all the nodes Halting parallel program mdrun on CPU 0 out of 16 --- my box size is 14*14*18. I used mdrun -rdd 1 , gromacs run without error is it correct or not? If you are sure that the maximum distance of your bonded interactions is 1nm, you can do that. It seems like mdrun was not able to find a decomposition automatically, try to give one by hand: $ mdrun -dd 2 2 4 Btw, your gromacs is 2 major versions behind, it might be a good idea to update. Christoph I get this error in NVT (Em run without error). Best Regards. Hamid Mosaddeghi -- View this message in context: http://gromacs.5086.n6.nabble.com/gromacs-VERSION-4-0-7-There-is-no-domain-decomposition-tp5006246.html Sent from the GROMACS Developers Forum mailing list archive at Nabble.com. -- gmx-developers mailing list gmx-develop...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-developers Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-requ...@gromacs.org. -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
to `cblas_ctrmm' ATL_larft.c:(.text+0x254): undefined reference to `cblas_ctrmm' /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In function `ATL_clarft_blockFR': ATL_larft.c:(.text+0x3bd): undefined reference to `cblas_ctrmm' ATL_larft.c:(.text+0x433): undefined reference to `cblas_cgemm' ATL_larft.c:(.text+0x481): undefined reference to `cblas_ctrmm' ATL_larft.c:(.text+0x4c4): undefined reference to `cblas_ctrmm' /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In function `ATL_clarft_blockBC': ATL_larft.c:(.text+0x643): undefined reference to `cblas_ctrmm' ATL_larft.c:(.text+0x69d): undefined reference to `cblas_cgemm' ATL_larft.c:(.text+0x6e8): undefined reference to `cblas_ctrmm' ATL_larft.c:(.text+0x72e): undefined reference to `cblas_ctrmm' /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In function `ATL_clarft_blockBR': ATL_larft.c:(.text+0x8c8): undefined reference to `cblas_ctrmm' ATL_larft.c:(.text+0x920): undefined reference to `cblas_cgemm' ATL_larft.c:(.text+0x96b): undefined reference to `cblas_ctrmm' ATL_larft.c:(.text+0x9b1): undefined reference to `cblas_ctrmm' /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In function `ATL_clarftFC': ATL_larft.c:(.text+0xcfb): undefined reference to `cblas_cdotc_sub' ATL_larft.c:(.text+0xdb3): undefined reference to `cblas_cdotu_sub' /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In function `ATL_clarftBC': ATL_larft.c:(.text+0xffd): undefined reference to `cblas_cdotc_sub' ATL_larft.c:(.text+0x10a9): undefined reference to `cblas_cdotu_sub' /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In function `ATL_clarftFR': ATL_larft.c:(.text+0x1368): undefined reference to `cblas_cdotc_sub' ATL_larft.c:(.text+0x1422): undefined reference to `cblas_cdotu_sub' /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In function `ATL_clarftBR': ATL_larft.c:(.text+0x165d): undefined reference to `cblas_cdotc_sub' ATL_larft.c:(.text+0x1713): undefined reference to `cblas_cdotu_sub' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTryCompileExec2027137673] Error 1 gmake[1]: Leaving directory `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' gmake: *** [cmTryCompileExec2027137673/fast] Error 2 Thanks, Evren -- gmx-developers mailing list gmx-develop...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-developers Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-requ...@gromacs.org. -- gmx-developers mailing list gmx-develop...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-developers Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-developers-requ...@gromacs.org. -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...
2013/3/6 Evren Yurtesen IB eyurt...@abo.fi: Hi Christoph, I thought problems in the compilation is more related to devs than users. But I sure can send mail first to users list in future. Thanks. I used the following to get it working. mkdir build_cmake cd build_cmake cmake .. -DCMAKE_INSTALL_PREFIX=/export/modules/apps/gromacs/4.6.1/mvapich2 This does not seem to work mkdir build_cmake cd build_cmake export CMAKE_INSTALL_PREFIX=/export/modules/apps/gromacs/4.6.1/mvapich2 cmake .. Was this the information you were looking for? That looks ok. I had a another look at the issue and I guess cmake's blas detention is a bit flaky, when it comes to static libraries. You are using liblapack.a, which has no link information, with liblapack.so it should have worked. Anyhow, thanks for reporting the issue. Christoph Thanks Evren On Wed, 6 Mar 2013, Christoph Junghans wrote: Hi Evren, please post these kind of questions on the users list as they are not really related to the development of gromacs. Concerning your question below, can you please post your cmake configure command line? Christoph 2013/3/6 Evren Yurtesen IB eyurt...@abo.fi: Sorry for the double post. I tried to post it from web and it said the post was not accepted to mailing list but then it arrived anyway. In addition the manual mentions setting CMAKE_INSTALL_PREFIX however this does not work when it is set it only works when given to cmake as a parameter with -DCMAKE_INSTALL_PREFIX=/something http://www.gromacs.org/Documentation/Installation_Instructions#4.3._CMake_advanced_options When I do an 'export CMAKE_INSTALL_PREFIX=/something' this is does not seem to propagate to configuration files, interestingly 'export CMAKE_PREFIX_PATH=/libpaths' seem to have the desired effect. Thanks, Evren On Wed, 6 Mar 2013, Evren Yurtesen IB wrote: Hello, I am not exactly sure if this is a bug but I realized that cmake system of gromacs couldnt find my ATLAS libraries. First problem was that it needed -lgfortran (and then -lcblas also) for compiling with gcc. The error I found in cmake error file can be found below. In addition while documentation suggests latest GCC versions, the only compatible version of GCC with CUDA 5.0 is GCC 4.6 but there doesnt seem to be any checks for this. Run Build Command:/usr/bin/gmake cmTryCompileExec3752895534/fast /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3752895534.dir/build.make CMakeFiles/cmTryCompileExec3752895534.dir/build gmake[1]: Entering directory `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -march=native -mtune=native -DCHECK_FUNCTION_EXISTS=dgemm_ -o CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o -c /usr/share/cmake/Modules/CheckFunctionExists.c Linking C executable cmTryCompileExec3752895534 /usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3752895534.dir/link.txt --verbose=1 /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -march=native -mtune=native -DCHECK_FUNCTION_EXISTS=dgemm_ CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o -o cmTryCompileExec3752895534 -rdynamic -Wl,-Bstatic -lf77blas -latlas -Wl,-Bdynamic /export/modules/devel/ATLAS/3.10.1/gnu/lib/libf77blas.a(xerbla.o): In function `xerbla_': xerbla.f:(.text+0x4a): undefined reference to `_gfortran_st_write' xerbla.f:(.text+0x5a): undefined reference to `_gfortran_transfer_character_write' xerbla.f:(.text+0x6a): undefined reference to `_gfortran_transfer_integer_write' xerbla.f:(.text+0x72): undefined reference to `_gfortran_st_write_done' xerbla.f:(.text+0x7b): undefined reference to `_gfortran_stop_string' collect2: error: ld returned 1 exit status gmake[1]: *** [cmTryCompileExec3752895534] Error 1 gmake[1]: Leaving directory `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' gmake: *** [cmTryCompileExec3752895534/fast] Error 2 After this the -lcblas was missing. Which caused the following errors. Run Build Command:/usr/bin/gmake cmTryCompileExec2027137673/fast /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2027137673.dir/build.make CMakeFiles/cmTryCompileExec2027137673.dir/build gmake[1]: Entering directory `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp' /usr/bin/cmake -E cmake_progress_report /home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp/CMakeFiles 1 Building C object CMakeFiles/cmTryCompileExec2027137673.dir/CheckFunctionExists.c.o /export/modules/compilers/gnu/gcc/4.7.2
[gmx-users] Re: gInstallation Problems with Gromacs4.6
Date: Fri, 1 Mar 2013 23:59:36 +0530
From: Abhishek Acharya aacha...@iitk.ac.in
Subject: [gmx-users] Installation Problems with Gromacs4.6
To: gromacs maillist gmx-users@gromacs.org
Message-ID:
2ca7063e41d6ddfa7ea411dc3cfe3ad3.squir...@webmail.iitk.ac.in
Content-Type: text/plain;charset=iso-8859-1
Hello Gromacs Users.
I have been trying to install Gromacs4.6 on our HPC facility. I think I
have correctly provided all the necessary mpi and fftw library paths. But
when i try to run configure it gives me the following error:
CMake Error at cmake/FindFFTW.cmake:105 (message):
Could not find fftwf_plan_r2r_1d in
/home/aacharya/softwares/fftw-3.3.3/lib/libfftw3f.so, take a look at the
error message in
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeError.log to
find out what went wrong. If you are using a static lib (.a) make sure
you
have specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
-DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
Call Stack (most recent call first):
CMakeLists.txt:894 (find_package)
As suggested here I looked into the CMakeError.log file of which I can't
make any sense.
Source file was:
#include mpi.h
int main(void) {
void* buf;
MPI_Allreduce(MPI_IN_PLACE, buf, 10, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD);
}
Determining if the function fftwf_plan_r2r_1d exists in the
/home/aacharya/softwares/fftw-3.3.3/lib failed with the following output:
Change Dir: /home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake cmTryCompileExec2668319475/fast
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec2668319475.dir/build.make
CMakeFiles/cmTryCompileExec2668319475.dir/build
gmake[1]: Entering directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_progress_report
/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp/CMakeFiles
1
Building C object
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d -o
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -c
/home/aacharya/softwares/cmake-2.8.10.2/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2668319475
/home/aacharya/softwares/cmake-2.8.10.2/bin/cmake -E cmake_link_script
CMakeFiles/cmTryCompileExec2668319475.dir/link.txt --verbose=1
/usr/bin/cc -Wextra -Wno-missing-field-initializers -Wno-sign-compare
-Wall -Wno-unused -Wunused-value
-DCHECK_FUNCTION_EXISTS=fftwf_plan_r2r_1d
-L/home/aacharya/softwares/fftw-3.3.3/lib
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o -o
cmTryCompileExec2668319475 -rdynamic -lm
Strange, there is supposed to be a -lfftw3f before -lm. Can you
tell us what your cmake command line was?
CMakeFiles/cmTryCompileExec2668319475.dir/CheckFunctionExists.c.o: In
function `main':
CheckFunctionExists.c:(.text+0x15): undefined reference to
`fftwf_plan_r2r_1d'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTryCompileExec2668319475] Error 1
gmake[1]: Leaving directory
`/home/aacharya/softwares/gromacs-4.6/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTryCompileExec2668319475/fast] Error 2
Kindly help. I tried installing 4.5.6 and it got installed without any
such problems. I need 4.6 because my tpr files are produced in Gromacs4.6
and I am using the Verlet cutoff scheme.
Thanks in advance
With Regards
Abhishek Acharya
--
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[gmx-users] Re: gmx-users Digest, Vol 106, Issue 69
Date: Wed, 13 Feb 2013 16:07:53 + From: Steven Neumann s.neuman...@gmail.com Subject: [gmx-users] Bond potential of atom groups To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAKZJqQEztzuGqm0t4=f37v+w-jioire0pz1tvdpj6cv7cyg...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear Gmx Users, I want to create coarse grained model. I need bond constant and equilibrium distance according to the equation V(r) =K (R - Req)^2 I wish to extract bonded potential between beads made out 3 atoms. I need Req and K. Equilibrium distance is straight forward - g_dist between COM or COG with index file conatining those 3 atoms. To match force constant K I need to extract bonded potential and try to fit to my parabolic curve. My question: How can I get bonded potential between beads of 3 atoms from AA simulation? Do I have to specify energy groups (energgrps) before the run in my mdp and then use g_energy? Have a look at the hexane example in the tutorials of the VOTCA package: https://code.google.com/p/votca/source/browse/?repo=csg-tutorials#hg%2Fhexane%2Fatomistic You will have to modify the mapping file (hexane.xml) a bit for your case, after that you can use the csg_boltzmann program to calculate the potential from the mapped distribution and try to fit the resulting potential table with the above mentioned functional form. (The VOTCA manual gives more details about these steps.) If you have further questions contact the VOTCA mailing list: vo...@googlegroups.com Cheers, Christoph Thank you Steven -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gromacs-4.6.tar.gz installation question
Date: Mon, 04 Feb 2013 15:32:17 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] gromacs-4.6.tar.gz installation question To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 51101ad1.3000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/4/13 3:30 PM, jeela keel wrote: *Dear All, I am trying to install gromacs, I dowloaded **gromacs-4.6.tar.gzftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gzand following the instruction in the following website http://www.gromacs.org/Documentation/Installation_Instructions#4._Doing_a_build_of_GROMACS I read the instraction but I am still kind of confused. Do I need to download both FFTW and CMake or just choose one of them for the gromacs installation? Both. FFTW is used for Fourier transforms. CMake is the compiler that builds the software. Also can I use FTTW **fftw-2.1.5.tar.gzftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gzinstead of **fftw-3.3.3.tar.gz ftp://ftp.fftw.org/pub/fftw/fftw-3.3.3.tar.gz becuase I also want to download Lammps in my computer that can only use fftw 2.1.5 We always advise using the newest version. There is no problem at all in maintaining different versions in different locations. In Gromacs-4.6 we have dropped support for fftw-2, which is legacy for nearly 13 years now, so you will need to install fftw-3 and btw. lammps supports fftw3 since Aug 2011. An alternative is to use gromacs build-in fftw (GMX_BUILD_OWN_FFTW=ON). Christoph -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: question about fftw3 in gromacs 4.6 installation
Date: Fri, 01 Feb 2013 19:00:02 -0500
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Re: question about fftw3 in gromacs 4.6
installation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 510c5702.5080...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2/1/13 5:26 PM, didymos wrote:
Hi Justin!
I had the same problem and I used your advise but I am not sure if this
entirely worked for me...
I used:
cmake -DGMX_MPI=ON DCMAKE_INSTALL_PREFIX=$HOME/gromacs
-DFFTWF_INCLUDE_DIR=$HOME/fftw/include
-DFFTWF_LIBRARY=$HOME/fftw/lib/libfftw3f.so -DCMAKE_PREFIX_PATH=$HOME/fftw/
..
The use of -DCMAKE_PREFIX_PATH eliminates the need for -DFFTWF_INCLUDE_DIR and
-DFFTWF_LIBRARY. Not that this is the source of your problem, but you can
certainly trim down your command.
and I got:
-- checking for module 'fftw3f'
-- found fftw3f, version 3.2.2
-- Looking for fftwf_plan_r2r_1d in
/home/users/didymos/fftw/lib/libfftw3f.so
-- Looking for fftwf_plan_r2r_1d in
/home/users/didymos/fftw/lib/libfftw3f.so - found
-- Looking for fftwf_have_simd_avx in
/home/users/didymos/fftw/lib/libfftw3f.so
-- Looking for fftwf_have_simd_avx in
/home/users/didymos/fftw/lib/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in
/home/users/didymos/fftw/lib/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in
/home/users/didymos/fftw/lib/libfftw3f.so - found
So it seems ok but I am not sure about first two lines:
-- checking for module 'fftw3f'
-- found fftw3f, version 3.2.2
it should be 3.3.3
Is there a different FFTW installed anywhere else on your system? I believe
the
first found fftw3f statement comes from pkgconfig detection, but this is
superseded by what you specify manually. Perhaps someone who is more familiar
with this element of the build system can comment.
Justin is 100% right, -DFFTWF_{INCLUDE_DIR,LIBRARY} supersedes,
whatever pkg-config finds before, you can see which library is used in
the output, in your case /home/users/didymos/fftw/lib/libfftw3f.so is
used.
One can also tweak the pkg-config's detection by including
/home/users/didymos/fftw in its search path:
export PKG_CONFIG_PATH=$HOME/fftw/lib/pkgconfig
and test if it works by
$ pkg-config --libs fftw3f
(I should add this trick to the wiki as setting PKG_CONFIG_PATH helps
to tweak the detection of fftw and gsl (when installed in same custom
location) with one variable.)
Christoph
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
Christoph Junghans
Web: http://www.compphys.de
--
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian
Date: Thu, 24 Jan 2013 01:07:04 +0100 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CANnYEw522dfPw5ELOr=xwqyn3xwoeujjpubh4bfc1r7ynhs...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi all, Let me clarify one thing: I highly doubt that the *gcc version* upgrade is what fixes your the issue, but rather the standard C++ library's version, as you can see the undefined symbols refer to GLIBCXX_3.4.15. Usually that is the case but for std::, the symbols are defined in libstdc++, which is part of the gcc package. $ strings /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/libstdc++.so | grep _M_hook _ZNSt6__norm15_List_node_base7_M_hookEPS0_ _ZNSt15_List_node_base7_M_hookEPS_ _ZNSt8__detail15_List_node_base7_M_hookEPS0_ _ZNSt9__cxx199815_List_node_base7_M_hookEPS0_ Christoph Of course, updating the compiler is a perfectly fine solution if you get the new (enough version of the) standard C++ library by doing so. Just wanted to clarify this for users bumping into this issue later. Cheers, -- Szilárd -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian
Date: Thu, 24 Jan 2013 15:55:13 +0100 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CANnYEw7Q3U_8aMyY=bzds0vveb_dg7fvc+pbkacoph8jzm4...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Let me add two more things. Note that we *always* compare performance and acceleration to our super-tuned state-of-the-art CPU code, which I can confidently say that is among the fastest if not the fastest to date, and never to some slow (CPU) implementation. Therefore, while other codes might be able to get 10-20x with GPUs and many x-es even with pre-Fermi (CC 2.0) cards, for obvious reasons we simply can't. Always check the following 10 points before believing the speed-up of any code: http://www.hpcwire.com/hpcwire/2011-12-13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus.html And Gromacs does a pretty fair comparison. Still you'll get high *absolute performance* regardless whether you can use CPU only or CPU+GPU, so this should be a decent deal, right? If anybody volunteers to add software-based floating point atomic operations for CC 2.0 and try running the current kernels on earlier hardware, I'm willing to give pointers, but I simply had no time to try it myself. This would enable using earlier cards, with a considerable performance penalty of emulated atomic ops (plus these cards are anyway slower), but it *might* be worth a try! Feel free to drop me a mail if anybody is interested. Cheers, -- Szilárd On Thu, Jan 24, 2013 at 3:48 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: On Thu, Jan 24, 2013 at 3:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/24/13 9:23 AM, James Starlight wrote: oh that was simply solved by upgrading of G++ :) the only problem which remains is the missing of support of mu GPU :( That time I've tried to start simulation on simply 2 cores CPU + geforce 9500 From md run I've obtained NOTE: Error occurred during GPU detection: CUDA driver version is insufficient for CUDA runtime version Can not use GPU acceleration, will fall back to CPU kernels. ED sampling will be performed! ED: Reading edi file new_a2a_pca_biased.edi ED: Note: Reference and average structure are composed of the same atom indices. ED: Found 1 ED group. Using 1 MPI thread Using 2 OpenMP threads No GPUs detected I've installed cuda-5.0 with driver NVRM version: NVIDIA UNIX x86_64 Kernel Module 304.54 Sat Sep 29 00:05:49 PDT 2012 that system works fine with the recent nvidia GPU's but has no support for GeForce 9500. GeForce 9500 cards have a compute capability of 1.1. The minimum required for Gromacs is 2.0 (noted in the installation instructions). Exactly! Anything below CC 2.0 lacks certain features that make those devices rather slow for our algorithms and therefore pretty much impractical. Cheers, -- Szilárd -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 105, Issue 119 *** -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian
Message: 5 Date: Tue, 22 Jan 2013 19:42:01 +0100 From: Szil?rd P?ll szilard.p...@cbr.su.se Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on Debian To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CANnYEw5=t=25hnZPfHpdJot7=3yncu1aegv7hcac3mut_75...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Tue, Jan 22, 2013 at 12:45 PM, James Starlight jmsstarli...@gmail.comwrote: Szilárd, Today I've tried to re-install cuda+gromacs and do apt-get distr-upgrade but the same error was obtained during gromacs I'm don't see how does the distribution upgrade relate to the issues you had (except if you have updated glibs to a newer version which is *still* incompatible with libcuda. You should probably try getting a more recent glibc and GCC version, one that libcuda is linked against. However, I'm not sure what the source of your problem is, so I can't suggest a certain solution. I had a similar problem on Gentoo Linux (https://bugs.gentoo.org/show_bug.cgi?id=452386), it helped to use a newer version of gcc (=4.6). Cheers, Christoph compilation. By the way where I could provide --add-needed option ? CMAKE_EXE_LINKER_FLAGS=-wl,--add-needed Cheers, Szilárd James 2013/1/21 Szilárd Páll szilard.p...@cbr.su.se: Szilárd -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Christoph Junghans Web: http://www.compphys.de -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
