from:"grantaka36"

[PyMOL] freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer'

2011-12-08 Thread grantaka36

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

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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-07 Thread grantaka36

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/
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Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-06 Thread grantaka36

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/
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[PyMOL] Installation PyMOL failure in Linux (CentOS)

2011-12-01 Thread grantaka36

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[³êÄ¢È¢øXgª}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
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Re: [PyMOL] how to activate pymol from remote server

2011-10-26 Thread grantaka36

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

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[PyMOL] how to activate pymol from remote server

2011-10-14 Thread grantaka36

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.
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[PyMOL] freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer'

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] Installation PyMOL failure in Linux (CentOS)

[PyMOL] Installation PyMOL failure in Linux (CentOS)

Re: [PyMOL] how to activate pymol from remote server

[PyMOL] how to activate pymol from remote server

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