Re: [ccp4bb] Coot crashes on CentOS 7.9
Dear Kay, Thanks for the reply. Some information regarding our system are as follows: >your processor came out in 2008, and it seems that Paul Emsley used compiler options that require newer capabilities than this processor has, likely in an attempt to speed up coot. Wikipedia says that AVX cameout in 2011 and AVX2 in 2013, so your processor supports neither extension. *Most probably this could be the reason.* >Do you still get >>> *** Cannot find the double-buffered visual. >>> *** Trying single-buffered visual. >? *Not anymore.* >glxinfo for my system: *name of display: :0display: :0 screen: 0direct rendering: Yesserver glx vendor string: NVIDIA Corporationserver glx version string: 1.4server glx extensions:* *..* *...* *Memory info (GL_NVX_gpu_memory_info):Dedicated video memory: 1536 MB Total available memory: 1536 MBCurrently available dedicated video memory: 1369 MBOpenGL vendor string: NVIDIA CorporationOpenGL renderer string: Quadro FX 4800/PCIe/SSE2OpenGL core profile version string: 3.3.0 NVIDIA 340.108OpenGL core profile shading language version string: 3.30 NVIDIA via Cg compilerOpenGL core profile context flags: (none)OpenGL core profile profile mask: core profileOpenGL core profile extensions: GL_ARB_ES2_compatibility, GL_ARB_ES3_compatibility,* The glxinfo is similar, however, I believe our system is too old. Thank you With regards Karthik On Thu, Apr 22, 2021 at 6:05 PM Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > Dear Karthik, > > your processor came out in 2008, and it seems that Paul Emsley used > compiler options that require newer capabilities than this processor has, > likely in an attempt to speed up coot. Wikipedia says that AVX came out in > 2011 and AVX2 in 2013, so your processor supports neither extension. > > Do you still get > >>> *** Cannot find the double-buffered visual. > >>> *** Trying single-buffered visual. > ? > > The way to debug this is to run > glxinfo > in a terminal and to compare the output (it is 1078 lines for my machine > ...) with that from a machine where the NVidia graphics works well. The > start of the output is most important and should agree; this is the output > for my machine: > > name of display: :0 > display: :0 screen: 0 > direct rendering: Yes > server glx vendor string: NVIDIA Corporation > server glx version string: 1.4 > server glx extensions: > ... > > Later it talks about the specific card and driver version; this will of > course differ from yours: > ... > Memory info (GL_NVX_gpu_memory_info): > Dedicated video memory: 8192 MB > Total available memory: 8192 MB > Currently available dedicated video memory: 7763 MB > OpenGL vendor string: NVIDIA Corporation > OpenGL renderer string: Quadro P4000/PCIe/SSE2 > OpenGL core profile version string: 4.6.0 NVIDIA 460.56 > OpenGL core profile shading language version string: 4.60 NVIDIA > OpenGL core profile context flags: (none) > OpenGL core profile profile mask: core profile > OpenGL core profile extensions: > GL_AMD_multi_draw_indirect, GL_AMD_seamless_cubemap_per_texture, > ... > > The ElRepo NVidia driver has worked well for us, but the driver directly > from NVidia should also be fine - but needs manual work after updating the > kernel IIRC. > > Best wishes, > Kay > > Am 22.04.2021 um 14:13 schrieb Karthikeyan Subramanian: > > Dear Kay, > > > > Thanks for the suggestions. > > > > The model name for the computer is "Intel(R) Xeon(R) CPU E5440 @ > 2.83GHz". > > > > As suggested, I downloaded and installed the latest ccp4 (7.1) which > bundles with coot 0.9.5. The coot works just fine with the latest ccp4 > bundle. > > > > I used the graphic driver from Nvidia package. I will try to use NVidia > driver from ELRepo. > > > > Time being I will use the one bundled with CCP4-7.1. > > > > Once again thanks for the help. > > > > With regards > > > > Karthik > > > > > > > > On 22-04-2021 02:18 pm, Kay Diederichs wrote: > >> Dear Karthikeyan Subramanian, > >> > >> which processor does your computer have? Look at the output of e.g. > "head -20 /proc/cpuinfo". What is "model name"? > >> > >> To my understanding, the main problem is > >> > >>>> *./coot: line 264: 5365 Illegal instruction (core dumped) > $coot_bin > >> This means that the compiler, when producing the coot binary, used > instructions that your processor does not understand (in the /proc/cpuinfo > output, some flags would be missing). This happens on old AMD processors > (unless such an
Re: [ccp4bb] Coot crashes on CentOS 7.9
Dear Kay, Thanks for the suggestions. The model name for the computer is "Intel(R) Xeon(R) CPU E5440 @ 2.83GHz". As suggested, I downloaded and installed the latest ccp4 (7.1) which bundles with coot 0.9.5. The coot works just fine with the latest ccp4 bundle. I used the graphic driver from Nvidia package. I will try to use NVidia driver from ELRepo. Time being I will use the one bundled with CCP4-7.1. Once again thanks for the help. With regards Karthik On 22-04-2021 02:18 pm, Kay Diederichs wrote: Dear Karthikeyan Subramanian, which processor does your computer have? Look at the output of e.g. "head -20 /proc/cpuinfo". What is "model name"? To my understanding, the main problem is *./coot: line 264: 5365 Illegal instruction (core dumped) $coot_bin This means that the compiler, when producing the coot binary, used instructions that your processor does not understand (in the /proc/cpuinfo output, some flags would be missing). This happens on old AMD processors (unless such an old processor is also used when compiling), and is the reason why CCP4 has its own distribution for these: go to http://www.ccp4.ac.uk/download/#os=linux and scroll down to "Legacy systems". If you indeed have an old AMD, just install CCP4 from there - CCP4 currently (at least the non-legacy distribution) has coot 0.9.5 . The other problem is *** Cannot find the double-buffered visual. *** Trying single-buffered visual. which points to the graphics driver; it is not properly installed. Are you using the NVidia driver from ElRepo? If not, you should try that. hope this helps, Kay On Thu, 22 Apr 2021 13:27:39 +0530, Karthikeyan Subramanian wrote: Dear CCP4 members, I am trying to install the coot-Linux-x86_64-scientific-linux-7.6-gtk2-python on CentOS 7.9 with Nvidia Quadro FX 4800 graphics card. Coot crashes soon after launching the window. The log file is shown below. Not sure what is missing. The only error I can see is *./coot: line 264: 5365 Illegal instruction (core dumped) $coot_bin "$@"". * The older version of coot (0.8.9.2) is working fine on the same machine. Thanks for the help. With regards Karthik IMTECH, Chandigarh == xray6 <1:14pm> 8% pwd /home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin xray6 <1:14pm> 9% ./coot (coot-bin:5365): GLib-GObject-WARNING **: 13:14:08.004: g_object_set_is_valid_property: object class 'GtkSettings' has no property named 'gtk-application-prefer-dark-theme' INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/programs/linux/ccp4-7.0/lib/data/monomers/ There are 153 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/m/MET.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/s/SER.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/t/THR.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/A.cif There are 2 data in /home/programs/linux/cc
[ccp4bb] Coot crashes on CentOS 7.9
Dear CCP4 members, I am trying to install the coot-Linux-x86_64-scientific-linux-7.6-gtk2-python on CentOS 7.9 with Nvidia Quadro FX 4800 graphics card. Coot crashes soon after launching the window. The log file is shown below. Not sure what is missing. The only error I can see is *./coot: line 264: 5365 Illegal instruction (core dumped) $coot_bin "$@"". * The older version of coot (0.8.9.2) is working fine on the same machine. Thanks for the help. With regards Karthik IMTECH, Chandigarh === xray6 <1:14pm> 8% pwd /home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin xray6 <1:14pm> 9% ./coot (coot-bin:5365): GLib-GObject-WARNING **: 13:14:08.004: g_object_set_is_valid_property: object class 'GtkSettings' has no property named 'gtk-application-prefer-dark-theme' INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/programs/linux/ccp4-7.0/lib/data/monomers/ There are 153 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/ALA.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASP.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASN.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/CYS.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLN.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLY.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLU.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/p/PHE.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/h/HIS.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/i/ILE.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/l/LYS.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/l/LEU.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/m/MET.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/m/MSE.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/p/PRO.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/ARG.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/s/SER.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/t/THR.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/v/VAL.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/t/TRP.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/t/TYR.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/p/PO4.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/s/SO4.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/GOL.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/CIT.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/e/EDO.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/A.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/C.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/G.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/u/U.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DA.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DC.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DG.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DT.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/h/HOH.cif There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/n/NA.cif Spacegroup: P 1 *** Cannot find the double-buffered visual. *** Trying single-buffered visual. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) INFO:: coot.py imported INFO:: coot_python initialized Running python script /home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Afternoon Person with no name, Welcome to Coot version 0.9.5 (set-display-intro-string "Good Afternoon Person with no name, Welcome to Coot version 0.9.5") Coot Python Scripting GUI code found and loaded. Coot Python Scripting GUI code found and loaded. (use-graphics-interface-state) Running python script /home/skarthik/.coot-preferences/0-coot-history.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) (set-display-intro-string "Good Afternoon Person with no name, Welcome to Coot version 0.8.9.2") (use-graphics-interface-state) (filter-fileselection-filenames-state) (get-active-map-drag-flag)
Re: [ccp4bb] How the IMEAN is calculated in scalepack2mtz
Thank you all for the information and F estimator write-up. With regards Karthik On 13-03-2017 03:56 AM, Phil Evans wrote: Sorry Ian, I was attributing this to Kevin apologies Phil On 12 Mar 2017, at 21:56, Ian Tickle <ianj...@gmail.com> wrote: Eleanor, Phil is right about the bias of the weighted mean, here's how I do it using a minimum mean-squared error estimator which seems to give more accurate results than either the unweighted or the weighted mean: http://staraniso.globalphasing.org/Optimal-F-estimator.pdf This is actually about Fmean but the same applies to Imean. This actually only makes a significant difference to the result if there's a big difference between sd(I+) and sd(I-), which is obviously not very common. Cheers -- Ian On 12 March 2017 at 17:58, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: You read: h k l IPLUS SIGIPLUS INEG SIGINEG Then program calculates this: SIGIMEAN = SIGIPLUS*SIGINEG/(SIGIPLUS+SIGINEG) IMEAN = (IPLUS/SIGIPLUS + INEG/SIGINEG)*SIGIMEAN ie: IMEAN = ( IPLUS*SIGINEG + INEG * SIGIPLUS ) / /(SIGIPLUS+SIGINEG) Is that the right thing to do? Not sure! Eleanor Dodson On 11 March 2017 at 15:18, Karthikeyan Subramanian <skarthi...@gmail.com> wrote: Dear CCP4bb, How IMEAN and SIGIMEAN is calculated in scalepack2mtz if the input is with anomalous intensity (obtained from HKL2000). Any guide/reference is highly appreciated. Thanks in advance, With regards Karthikeyan S. Principal Scientist IMTECH, Chandigarh
[ccp4bb] How the IMEAN is calculated in scalepack2mtz
Dear CCP4bb, How IMEAN and SIGIMEAN is calculated in scalepack2mtz if the input is with anomalous intensity (obtained from HKL2000). Any guide/reference is highly appreciated. Thanks in advance, With regards Karthikeyan S. Principal Scientist IMTECH, Chandigarh
