[PyMOL] freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer'
Hi Thomas and all, I branched the thread from the original: http://sourceforge.net/mailarchive/message.php?msg_id=28507590 After PyMOL running, console says: freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer' but I will try to check and contact here as another issue if not succeeded. KB-order .mol2 can be opened, but some large (MB-order) .pdb cannot and shutdown with 'abrupt termination.' glxinfo | grep direct direct rendering: No do you have a graphics driver with direct rendering support installed? No. I think firmly caused by lack of graphic driver. http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg05060.html OpenGL graphics engine: GL_VENDOR: Intel GL_RENDERER: Intel 945G GL_VERSION: 1.2 (1.4.0 - Build 4.14.10.4543) Have anyone experienced some workaround for above driver? (Might be fit the following, but I cannot find how to install appropriate one) http://intellinuxgraphics.org/download.html Regards, Masataka -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)
Dear Thomas and all advisers, Thanks for all, I've got installed pymol in CentOS5 from EPEL repository. Turning back to the package list by Yum Extender (yumex), I found 'pymol' appeared as http://lockerz.com/s/162790999 after http://lockerz.com/s/162790733 cf.) - Might need installed 'epel*' # rpm -i http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm - 'yumex' can be installed: # yum install yumex Can I add this information to pymolwiki (Need an account) ? http://www.pymolwiki.org/index.php/Linux_Install After PyMOL running, console says: freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer' but I will try to check and contact here as another issue if not succeeded. Regards, Masataka 2011/12/6 grantaka36 grantak...@gmail.com: Dear Thomas, Thanks for good pointing for the weird problem, which I couldn't notice at all. You do compile with -D_FORTIFY_SOURCE=2, could you remove that? I'm afraid, I know not related PyMOL itself, but I wish to know how to do that. Searching 'setup.py', 'setup2.py' or some 'Makefile*' with the string 'D_FORTIFY_SOURCE' or 'gcc' returned no matches. And Zhijian and Andreas, Thank you for advices through your experiences, I will pursue at first as Thomas advised. Regards, Masataka 2011/12/5 Andreas Förster docandr...@gmail.com: Dear Masataka, a few months ago, I upgraded most of our computers from RHEL 5.x to 6.1. If version 6 of CentOS (free RHEL clone) is out, I would highly recommend, no I would urge you, to upgrade as well. RHEL and CentOS are rock-solid operating systems, but their libraries and dependencies show their age. Andreas On 05/12/2011 1:50, grantaka36 wrote: Hi, Marius, Troels and David, I appreciate very much for guiding, tried in three ways but no success currently. - I also think some difference on distributions (CentOS 5 here,) trapped at function 'IsosurfGetRange' Does anyone have information to workaround? - Do you think if any dependency on Python version (2.4.3 here)? Attached '20111205_script_and_error.zip' is for information sharing: - 'install_pymol.sh' : followed by below, some package name modified for CentOS http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support - 'install_pymol_sh_error.txt' layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro fprintf layer0/Isosurf.c: In function 'IsosurfGetRange': - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5 instead of 4.4 - 'install_pymol_gcc45_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf - 'compile_pymol.sh' : again by initial trying http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source - 'compile_pymol_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf Regards, Masataka -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)
Dear Thomas, Thanks for good pointing for the weird problem, which I couldn't notice at all. You do compile with -D_FORTIFY_SOURCE=2, could you remove that? I'm afraid, I know not related PyMOL itself, but I wish to know how to do that. Searching 'setup.py', 'setup2.py' or some 'Makefile*' with the string 'D_FORTIFY_SOURCE' or 'gcc' returned no matches. And Zhijian and Andreas, Thank you for advices through your experiences, I will pursue at first as Thomas advised. Regards, Masataka 2011/12/5 Andreas Förster docandr...@gmail.com: Dear Masataka, a few months ago, I upgraded most of our computers from RHEL 5.x to 6.1. If version 6 of CentOS (free RHEL clone) is out, I would highly recommend, no I would urge you, to upgrade as well. RHEL and CentOS are rock-solid operating systems, but their libraries and dependencies show their age. Andreas On 05/12/2011 1:50, grantaka36 wrote: Hi, Marius, Troels and David, I appreciate very much for guiding, tried in three ways but no success currently. - I also think some difference on distributions (CentOS 5 here,) trapped at function 'IsosurfGetRange' Does anyone have information to workaround? - Do you think if any dependency on Python version (2.4.3 here)? Attached '20111205_script_and_error.zip' is for information sharing: - 'install_pymol.sh' : followed by below, some package name modified for CentOS http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support - 'install_pymol_sh_error.txt' layer0/Isosurf.c:2197:1: error: unterminated argument list invoking macro fprintf layer0/Isosurf.c: In function 'IsosurfGetRange': - 'install_pymol_gcc45.sh' - aiming to use default installed gcc4.5 instead of 4.4 - 'install_pymol_gcc45_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf - 'compile_pymol.sh' : again by initial trying http://www.pymolwiki.org/index.php/Linux_Install#Install_from_source - 'compile_pymol_sh_error.txt' layer0/Isosurf.c: In function 'IsosurfGetRange': layer0/Isosurf.c:2197:0: error: unterminated argument list invoking macro fprintf Regards, Masataka -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- Cloud Services Checklist: Pricing and Packaging Optimization This white paper is intended to serve as a reference, checklist and point of discussion for anyone considering optimizing the pricing and packaging model of a cloud services business. Read Now! http://www.accelacomm.com/jaw/sfnl/114/51491232/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Installation PyMOL failure in Linux (CentOS)
Referring the following, I'm trying to install PyMOL 1.4.1 with attached 'compile_pymol.sh', but no success. Would you please help to finish installation, or give me some advices? If information inadequate, please contact me. http://www.pymolwiki.org/index.php/Linux_Install - Requirements - Get latest Source from SVN - Compile and install - Problems - gcc-4.5 is broken for pymol install, use gcc-4.4 -- My distribution has gcc4.5, so installed /usr/bin/gcc44, /usr/bin/g++44. Attached 'install_error.txt' gathers some information: - Original module files are in $HOME/install_module/pymol-archive - Intends to install in $HOME/pymol-svn - Original log has some Japanese messages so I added /* means ... */ Regards, Masataka # -- [user01@rain02 etc]$ cat /etc/issue CentOS release 5.5 (Final) Kernel \r on an \m # -- [user01@rain02 etc]$ python -V Python 2.4.3 [user01@rain02 etc]$ # -- [user01@rain02 pymol-archive]$ gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.5.1/lto-wrapper Target: x86_64-unknown-linux-gnu /* means config option */: ./configure -disable-multilib --with-gmp=/usr/local --with-mpfr=/usr/local --with-mpc=/usr/local /* means thread model */: posix gcc version 4.5.1 (GCC) # -- [user01@rain02 pymol-archive]$ which gcc44 /usr/bin/gcc44 [user01@rain02 pymol-archive]$ which g++44 /usr/bin/g++44 [user01@rain02 pymol-archive]$ export CC=/usr/bin/gcc44 [user01@rain02 pymol-archive]$ echo $CC /usr/bin/gcc44 [user01@rain02 pymol-archive]$ ./compile_pymol.sh running build running build_py package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) package init file 'modules/web/javascript/__init__.py' not found (or not a regular file) running build_ext building 'pymol._cmd' extension /usr/bin/gcc44 -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.4 -c layer0/Isosurf.c -o build/temp.linux-x86_64-2.4/layer0/Isosurf.o -ffast-math -funroll-loops -O3 layer0/Isosurf.c:2197:1: error: I[³êĢȢøXgª}N fprintf ðN®µæ¤ÆµÜµ½ /* means unterminated argument list invoking macro \fprintf\ */ layer0/Isosurf.c: In function eIsosurfGetRangef: layer0/Isosurf.c:765: x: /* means warning */ statement with no effect layer0/Isosurf.c:765: error: expected e;f at end of input layer0/Isosurf.c:765: error: expected declaration or statement at end of input layer0/Isosurf.c:765: error: expected declaration or statement at end of input layer0/Isosurf.c:765: error: expected declaration or statement at end of input layer0/Isosurf.c:764: x: unused variable eclampedf layer0/Isosurf.c:763: x: unused variable ebf layer0/Isosurf.c:763: x: unused variable eaf layer0/Isosurf.c:762: x: unused variable eimixf layer0/Isosurf.c:762: x: unused variable emixf layer0/Isosurf.c:761: x: unused variable eimxf layer0/Isosurf.c:761: x: unused variable eimnf layer0/Isosurf.c:760: x: unused variable ermxf layer0/Isosurf.c:760: x: unused variable ermnf error: command '/usr/bin/gcc44' failed with exit status 1 [user01@rain02 pymol-archive]$ compile_pymol.sh Description: Bourne shell script -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] how to activate pymol from remote server
Hi Thomas, Troels and Alvin, I appreciate your instant and detail advices to my problem, I got succeeded - scripting in [C] enabled activate pymol in [S]. As Troels says, I agree it's not pymol issue indeed, and sorry for contaminating some questions to here list. What is done: laptop$ ssh -l (loginName) (remote-machine) # tried ssh -Y or -X, but simply this succeeded login@(remote-machine)$ export DISPLAY=:0.0# it seemed the point, somehow not enough laptop:0.0 login@(remote-machine)$ xclock #worked login@(remote-machine)$ pymol #worked Referred from: laptop# xhost +remote-machine laptop# ssh -l loginName remote-machine login@remote-machine# export DISPLAY=laptop:0.0 login@remote-machine# xterm - see if it works login@remote-machine# pymol More I want to quit pymol GUI from [C], but 'pymol -qip' will be fit as Thomas says. Thanks again for all. Regards, Masataka -- The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] how to activate pymol from remote server
Dear list members, Would you please tell me the way, how to activate pymol from remote server? i.e. how to start pymol in [S] by scripting from [C] -- - From Windows client [C], SSH2 logging in to the remote server [S] (Linux x64, Ubuntu 10) - [S] -- installed PyMOL 1.2 r2, PATH includes '/usr/bin/pymol' so only 'pymol' entering enable to activate pymol GUI -- 'python' returns -- Python 2.6.6 (r266:84292, Sep 15 2010, 16:22:56) -- [GCC 4.4.5] on linux2 - [C] -- first trying the following: PYMOL_PATH=/usr/bin/pymol HOST_ID=`uname -n` pymol -R -display:${HOST_ID}:0.0 -- returns: Traceback (most recent call last): File /usr/lib/python2.6/runpy.py, line 122, in _run_module_as_main __main__, fname, loader, pkg_name) File /usr/lib/python2.6/runpy.py, line 34, in _run_code exec code in run_globals File /usr/lib/pymodules/python2.6/pymol/__init__.py, line 495, in module invocation.parse_args(pymol_argv) File /usr/lib/pymodules/python2.6/pymol/invocation.py, line 251, in parse_args options.stereo_mode = int(av.pop()) IndexError: pop from empty list -- By referring, http://www.pymolwiki.org/index.php/Launching_PyMOL#Launching_PyMOL_from_an_external_application If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you can launch PyMOL from an external Python program But I don't know which path to designate LD_LIBRARY_PATH and TCL_LIBRARY Regards, Masataka -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2d-oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net