25 March 2014

568. PyMol troubles in Jessie -- no solutions [update]

I and linux are not on speaking terms at the moment. My main issue right now is that the routing that I set up a long time ago (http://verahill.blogspot.com.au/2012/02/debian-testing-wheezy-64-configuring.html) no longer works properly -- yes, I can see the subnets, but the routing table is wrong, and traffic is routed over the wrong physical interface which leads to a significant slowdown.

In addition, pymol is unusable on my laptop which is running debian jessie. I'm not the only one with pymol related issues either -- follow the thread at the end of http://verahill.blogspot.com.au/p/miscellaneous.html and you will see another example of pymol troubles, troubles which I accidentally reproduced in the virtual machine later in this post. Anyway, these are unsolved issues but I post them here in case other people are wondering whether they are the only ones. I might even muster the courage to submit a bug report to debian although the first issue is definitely present in upstreams...and I think that the second one is as well. Unfortunately, pymol isn't quite free software and the online support doesn't appear to be as good as for many traditional FOSS packages.

Either way, here are some observations:

On a physical machine (Lenovo Thinkpad SL410 running Jessie:
UPDATE 26/3/2014: this works now after doing a full upgrade/dist-upgrade. Not sure what did it -- no obvious package that would've fixed it. The issue below with gallium remains though.

Version 1.7.0.0 on Linux niobium 3.11-2-amd64 #1 SMP Debian 3.11.10-1 (2013-12-04) x86_64 GNU/Linux.
Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: Intel Open Source Technology Center GL_RENDERER: Mesa DRI Mobile Intel GM45 Express Chipset GL_VERSION: 2.1 Mesa 9.2.2 Adjusting settings to improve performance for Intel cards. Detected 2 CPU cores. Enabled multithreaded rendering.

Building the upstreams version doesn't solve the issue.

inxi -G:
Graphics: Card: Intel Mobile 4 Series Integrated Graphics Controller X.Org: 1.15.0 drivers: intel (unloaded: fbdev,vesa) Resolution: 1366x768@60.0hz GLX Renderer: Mesa DRI Mobile Intel GM45 Express GLX Version: 2.1 Mesa 9.2.2

In a debian testing virtual machine (virtual box) running jessie:
Default DE seems to be Xfce. Before installing gnome i.e. in Xfce:
X Error of failed request: 0 Major opcode of failed request: 155 (GLX) Minor opcode of failed request: 26 (X_GLXMakeContextCurrent) Serial number of failed request: 49 Current serial number in output stream: 49 PyMOL: abrupt program termination.
After installing gnome:
Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.30. OpenGL graphics engine: GL_VENDOR: VMware, Inc. GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 128 bits) GL_VERSION: 2.1 Mesa 9.2.2 pure virtual method called
and a normal window is opened:
While it says v 1.6.x it is version 1.7.0.0 and it says so in the terminal output -- just not in the fancy figure.


However, on loading any structure (e.g. xyz or pdb -- even as small as methane):
OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.30. OpenGL graphics engine: GL_VENDOR: VMware, Inc. GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 128 bits) GL_VERSION: 2.1 Mesa 9.2.2 CmdLoad: "/home/me/Downloads/methane.pdb" loaded as "methane". Segmentation fault
Running catchsegv gives a lot of output -- see bottom of this post.

I next installed the guest additions from the debian repos using
sudo apt-get install virtualbox-guest-*
(the guest additions that are installable via virtualbox itself fail to build on kernel 3.13) and rebooted.

At this point pymol shows
me@debian:~$ pymol ~/Downloads/methane.pdb OpenGL Warning: glFlushVertexArrayRangeNV not found in mesa table OpenGL Warning: glVertexArrayRangeNV not found in mesa table OpenGL Warning: glCombinerInputNV not found in mesa table OpenGL Warning: glCombinerOutputNV not found in mesa table OpenGL Warning: glCombinerParameterfNV not found in mesa table OpenGL Warning: glCombinerParameterfvNV not found in mesa table OpenGL Warning: glCombinerParameteriNV not found in mesa table OpenGL Warning: glCombinerParameterivNV not found in mesa table OpenGL Warning: glFinalCombinerInputNV not found in mesa table OpenGL Warning: glGetCombinerInputParameterfvNV not found in mesa table OpenGL Warning: glGetCombinerInputParameterivNV not found in mesa table OpenGL Warning: glGetCombinerOutputParameterfvNV not found in mesa table OpenGL Warning: glGetCombinerOutputParameterivNV not found in mesa table OpenGL Warning: glGetFinalCombinerInputParameterfvNV not found in mesa table OpenGL Warning: glGetFinalCombinerInputParameterivNV not found in mesa table OpenGL Warning: glDeleteFencesNV not found in mesa table OpenGL Warning: glFinishFenceNV not found in mesa table OpenGL Warning: glGenFencesNV not found in mesa table OpenGL Warning: glGetFenceivNV not found in mesa table OpenGL Warning: glIsFenceNV not found in mesa table OpenGL Warning: glSetFenceNV not found in mesa table OpenGL Warning: glTestFenceNV not found in mesa table PyMOL(TM) Molecular Graphics System, Version 1.7.0.0. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help " for information on a specific command. Hit ESC anytime to toggle between text and graphics. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 4.20. OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU OpenGL graphics engine: GL_VENDOR: Humper GL_RENDERER: Chromium GL_VERSION: 2.1 Chromium 1.9 CmdLoad: "/home/me/Downloads/methane.pdb" loaded as "methane". OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU
and the molecule shows up briefly before the window goes black, which constitutes a bit of progress.

Closing the program gives
PyMOL: normal program termination. Segmentation fault

catchsegv output using the gallium driver
PyMOL(TM) Molecular Graphics System, Version 1.7.0.0. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org". Enter "help" for a list of commands. Enter "help " for information on a specific command. Hit ESC anytime to toggle between text and graphics. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.30. OpenGL graphics engine: GL_VENDOR: VMware, Inc. GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.3, 128 bits) GL_VERSION: 2.1 Mesa 9.2.2 ExecutiveLoad: "methane.xyz" loaded as "methane", through state 1. Segmentation fault *** Segmentation fault Register dump: RAX: 0000000002214e08 RBX: 000000000000ffff RCX: 0000000000000000 RDX: 00007f1db5b69640 RSI: 00000000ffffffff RDI: 00007fff4c2e7d60 RBP: 00007fff4c0e7d80 R8 : 0000000000000000 R9 : 0000000000000000 R10: 0000000002088a50 R11: 000000000208c940 R12: 000000000248b650 R13: 00007f1dafad70fc R14: 00007fff4c0e7c94 R15: 0000000000000000 RSP: 00007fff4c0e7c10 RIP: 00007f1daf8f4202 EFLAGS: 00010206 CS: 0033 FS: 0000 GS: 0000 Trap: 0000000e Error: 00000006 OldMask: 00000000 CR2: 4c2eb110 FPUCW: 0000037f FPUSW: 00000000 TAG: 00000000 RIP: 00000000 RDP: 00000000 ST(0) 0000 0000000000000000 ST(1) 0000 0000000000000000 ST(2) 0000 0000000000000000 ST(3) 0000 0000000000000000 ST(4) 0000 0000000000000000 ST(5) 0000 0000000000000000 ST(6) 0000 0000000000000000 ST(7) 0000 0000000000000000 mxcsr: 9ffb XMM0: 00000000000000000000000000000000 XMM1: 00000000000000000000000000000000 XMM2: 00000000000000000000000000000000 XMM3: 00000000000000000000000000000000 XMM4: 00000000000000000000000000000000 XMM5: 00000000000000000000000000000000 XMM6: 00000000000000000000000000000000 XMM7: 00000000000000000000000000000000 XMM8: 00000000000000000000000000000000 XMM9: 00000000000000000000000000000000 XMM10: 00000000000000000000000000000000 XMM11: 00000000000000000000000000000000 XMM12: 00000000000000000000000000000000 XMM13: 00000000000000000000000000000000 XMM14: 00000000000000000000000000000000 XMM15: 00000000000000000000000000000000 Backtrace: /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2ed202)[0x7f1daf8f4202] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2e8dfe)[0x7f1daf8efdfe] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2f1a69)[0x7f1daf8f8a69] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x338f6f)[0x7f1daf93ff6f] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x33a059)[0x7f1daf941059] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(llvmpipe_update_fs+0x99d)[0x7f1daf945bbd] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(llvmpipe_update_derived+0x1a0)[0x7f1daf93e9c0] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(lp_setup_update_state+0xe8)[0x7f1daf938d08] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x33726b)[0x7f1daf93e26b] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x208c40)[0x7f1daf80fc40] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x20908e)[0x7f1daf81008e] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x201f94)[0x7f1daf808f94] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2049fa)[0x7f1daf80b9fa] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x200235)[0x7f1daf807235] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2010e4)[0x7f1daf8080e4] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2f7285)[0x7f1daf8fe285] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x2f7454)[0x7f1daf8fe454] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x212b21)[0x7f1daf819b21] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x20b916)[0x7f1daf812916] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x20bd96)[0x7f1daf812d96] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x326a72)[0x7f1daf92da72] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x14fb1c)[0x7f1daf756b1c] /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so(+0x1294c4)[0x7f1daf7304c4] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0xf3bb9)[0x7f1db4c16bb9] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(CGORenderGL+0x745)[0x7f1db4c359b5] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x1a5b7c)[0x7f1db4cc8b7c] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(CoordSetRender+0x323)[0x7f1db4d56253] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x1e5203)[0x7f1db4d08203] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(SceneRenderAllObject+0xc1)[0x7f1db4beb291] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0xc8898)[0x7f1db4beb898] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(DoRendering+0x204)[0x7f1db4bebe54] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(SceneRender+0x13c7)[0x7f1db4bf2a77] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(OrthoDoDraw+0x104c)[0x7f1db4c918ec] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(ExecutiveDrawNow+0xc1)[0x7f1db4df4ab1] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(PyMOL_DrawWithoutLock+0x16e)[0x7f1db4e5a73e] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x3233a0)[0x7f1db4e463a0] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x3241fc)[0x7f1db4e471fc] /usr/lib/x86_64-linux-gnu/libglut.so.3(+0x22834)[0x7f1db3cd7834] /usr/lib/x86_64-linux-gnu/libglut.so.3(fgEnumWindows+0x39)[0x7f1db3cdb279] /usr/lib/x86_64-linux-gnu/libglut.so.3(glutMainLoopEvent+0x11c)[0x7f1db3cd7d7c] /usr/lib/x86_64-linux-gnu/libglut.so.3(glutMainLoop+0xa1)[0x7f1db3cd8671] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x324b30)[0x7f1db4e47b30] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(main_shared+0x88)[0x7f1db4e48698] /usr/lib/python2.7/dist-packages/pymol/_cmd.so(+0x3039b4)[0x7f1db4e269b4] python2.7(PyEval_EvalFrameEx+0x42d)[0x51f18d] python2.7(PyEval_EvalCodeEx+0x2ac)[0x53bd7c] python2.7(PyEval_EvalFrameEx+0x7f6)[0x51f556] python2.7(PyEval_EvalCodeEx+0x2ac)[0x53bd7c] python2.7(PyEval_EvalCode+0x32)[0x5b0b62] python2.7(PyEval_EvalFrameEx+0x4f5c)[0x523cbc] python2.7(PyEval_EvalCodeEx+0x2ac)[0x53bd7c] python2.7(PyEval_EvalFrameEx+0x7f6)[0x51f556] python2.7[0x4e738a] python2.7(PyObject_Call+0x36)[0x55f4c6] python2.7[0x41e910] python2.7(Py_Main+0x898)[0x44bfba] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f1db57e7b45] python2.7[0x57b33e] Memory map: 00400000-006bc000 r-xp 00000000 08:01 274159 /usr/bin/python2.7 008bc000-008bd000 r--p 002bc000 08:01 274159 /usr/bin/python2.7 008bd000-00932000 rw-p 002bd000 08:01 274159 /usr/bin/python2.7 00932000-00944000 rw-p 00000000 00:00 0 01316000-02a92000 rw-p 00000000 00:00 0 [heap] 7f1da4000000-7f1da465c000 rw-p 00000000 00:00 0 7f1da465c000-7f1da8000000 ---p 00000000 00:00 0 7f1da8e6b000-7f1da8eeb000 rw-p 00000000 00:00 0 7f1da913e000-7f1da917e000 rw-p 00000000 00:00 0 7f1da917e000-7f1da91fe000 rwxp 00000000 00:00 0 7f1da91fe000-7f1da936b000 rw-p 00000000 00:00 0 7f1da936b000-7f1da9373000 r-xp 00000000 08:01 274422 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so 7f1da9373000-7f1da9572000 ---p 00008000 08:01 274422 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so 7f1da9572000-7f1da9573000 r--p 00007000 08:01 274422 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so 7f1da9573000-7f1da9574000 rw-p 00008000 08:01 274422 /usr/lib/python2.7/lib-dynload/_ssl.x86_64-linux-gnu.so 7f1da9574000-7f1da9580000 r-xp 00000000 08:01 521244 /lib/x86_64-linux-gnu/libnss_files-2.18.so 7f1da9580000-7f1da977f000 ---p 0000c000 08:01 521244 /lib/x86_64-linux-gnu/libnss_files-2.18.so 7f1da977f000-7f1da9780000 r--p 0000b000 08:01 521244 /lib/x86_64-linux-gnu/libnss_files-2.18.so 7f1da9780000-7f1da9781000 rw-p 0000c000 08:01 521244 /lib/x86_64-linux-gnu/libnss_files-2.18.so 7f1da9781000-7f1da978b000 r-xp 00000000 08:01 521253 /lib/x86_64-linux-gnu/libnss_nis-2.18.so 7f1da978b000-7f1da998a000 ---p 0000a000 08:01 521253 /lib/x86_64-linux-gnu/libnss_nis-2.18.so 7f1da998a000-7f1da998b000 r--p 00009000 08:01 521253 /lib/x86_64-linux-gnu/libnss_nis-2.18.so 7f1da998b000-7f1da998c000 rw-p 0000a000 08:01 521253 /lib/x86_64-linux-gnu/libnss_nis-2.18.so 7f1da998c000-7f1da9993000 r-xp 00000000 08:01 521246 /lib/x86_64-linux-gnu/libnss_compat-2.18.so 7f1da9993000-7f1da9b92000 ---p 00007000 08:01 521246 /lib/x86_64-linux-gnu/libnss_compat-2.18.so 7f1da9b92000-7f1da9b93000 r--p 00006000 08:01 521246 /lib/x86_64-linux-gnu/libnss_compat-2.18.so 7f1da9b93000-7f1da9b94000 rw-p 00007000 08:01 521246 /lib/x86_64-linux-gnu/libnss_compat-2.18.so 7f1da9b94000-7f1da9b95000 ---p 00000000 00:00 0 7f1da9b95000-7f1daa415000 rw-p 00000000 00:00 0 [stack:5355] 7f1daa415000-7f1daa595000 rwxp 00000000 00:00 0 7f1daa595000-7f1daa615000 rw-p 00000000 00:00 0 7f1daa615000-7f1daa616000 ---p 00000000 00:00 0 7f1daa616000-7f1daae16000 rw-p 00000000 00:00 0 [stack:5354] 7f1daae16000-7f1daae1f000 r-xp 00000000 08:01 270355 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0 7f1daae1f000-7f1dab01e000 ---p 00009000 08:01 270355 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0 7f1dab01e000-7f1dab01f000 r--p 00008000 08:01 270355 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0 7f1dab01f000-7f1dab020000 rw-p 00009000 08:01 270355 /usr/lib/x86_64-linux-gnu/libXrender.so.1.3.0 7f1dab020000-7f1dab022000 r-xp 00000000 08:01 277479 /usr/lib/x86_64-linux-gnu/libXss.so.1.0.0 7f1dab022000-7f1dab222000 ---p 00002000 08:01 277479 /usr/lib/x86_64-linux-gnu/libXss.so.1.0.0 7f1dab222000-7f1dab223000 rw-p 00002000 08:01 277479 /usr/lib/x86_64-linux-gnu/libXss.so.1.0.0 7f1dab223000-7f1dab25d000 r-xp 00000000 08:01 270332 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.8.0 7f1dab25d000-7f1dab45c000 ---p 0003a000 08:01 270332 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.8.0 7f1dab45c000-7f1dab45e000 r--p 00039000 08:01 270332 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.8.0 7f1dab45e000-7f1dab45f000 rw-p 0003b000 08:01 270332 /usr/lib/x86_64-linux-gnu/libfontconfig.so.1.8.0 7f1dab45f000-7f1dab473000 r-xp 00000000 08:01 275893 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.1 7f1dab473000-7f1dab673000 ---p 00014000 08:01 275893 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.1 7f1dab673000-7f1dab674000 rw-p 00014000 08:01 275893 /usr/lib/x86_64-linux-gnu/libXft.so.2.3.1 7f1dab674000-7f1dab689000 r-xp 00000000 08:01 521239 /lib/x86_64-linux-gnu/libnsl-2.18.so 7f1dab689000-7f1dab888000 ---p 00015000 08:01 521239 /lib/x86_64-linux-gnu/libnsl-2.18.so 7f1dab888000-7f1dab889000 r--p 00014000 08:01 521239 /lib/x86_64-linux-gnu/libnsl-2.18.so 7f1dab889000-7f1dab88a000 rw-p 00015000 08:01 521239 /lib/x86_64-linux-gnu/libnsl-2.18.so 7f1dab88a000-7f1dab88c000 rw-p 00000000 00:00 0 7f1dab88c000-7f1dab9a5000 r-xp 00000000 08:01 299562 /usr/lib/x86_64-linux-gnu/libtcl8.5.so 7f1dab9a5000-7f1dabba5000 ---p 00119000 08:01 299562 /usr/lib/x86_64-linux-gnu/libtcl8.5.so 7f1dabba5000-7f1dabba9000 r--p 00119000 08:01 299562 /usr/lib/x86_64-linux-gnu/libtcl8.5.so 7f1dabba9000-7f1dabbb0000 rw-p 0011d000 08:01 299562 /usr/lib/x86_64-linux-gnu/libtcl8.5.so 7f1dabbb0000-7f1dabbb1000 rw-p 00000000 00:00 0 7f1dabbb1000-7f1dabcdd000 r-xp 00000000 08:01 299568 /usr/lib/x86_64-linux-gnu/libtk8.5.so 7f1dabcdd000-7f1dabedc000 ---p 0012c000 08:01 299568 /usr/lib/x86_64-linux-gnu/libtk8.5.so 7f1dabedc000-7f1dabeea000 r--p 0012b000 08:01 299568 /usr/lib/x86_64-linux-gnu/libtk8.5.so 7f1dabeea000-7f1dabefb000 rw-p 00139000 08:01 299568 /usr/lib/x86_64-linux-gnu/libtk8.5.so 7f1dabefb000-7f1dabefc000 rw-p 00000000 00:00 0 7f1dabefc000-7f1dac003000 r-xp 00000000 08:01 299629 /usr/lib/libBLT.2.4.so.8.5 7f1dac003000-7f1dac203000 ---p 00107000 08:01 299629 /usr/lib/libBLT.2.4.so.8.5 7f1dac203000-7f1dac204000 r--p 00107000 08:01 299629 /usr/lib/libBLT.2.4.so.8.5 7f1dac204000-7f1dac221000 rw-p 00108000 08:01 299629 /usr/lib/libBLT.2.4.so.8.5 7f1dac221000-7f1dac222000 rw-p 00000000 00:00 0 7f1dac222000-7f1dac22e000 r-xp 00000000 08:01 299653 /usr/lib/python2.7/lib-dynload/_tkinter.so 7f1dac22e000-7f1dac42d000 ---p 0000c000 08:01 299653 /usr/lib/python2.7/lib-dynload/_tkinter.so 7f1dac42d000-7f1dac42e000 r--p 0000b000 08:01 299653 /usr/lib/python2.7/lib-dynload/_tkinter.so 7f1dac42e000-7f1dac430000 rw-p 0000c000 08:01 299653 /usr/lib/python2.7/lib-dynload/_tkinter.so 7f1dac430000-7f1dac4b0000 rw-p 00000000 00:00 0 7f1dac4b0000-7f1dacf30000 rwxp 00000000 00:00 0 7f1dacf30000-7f1dad031000 rw-p 00000000 00:00 0 7f1dad032000-7f1dad132000 rwxp 00000000 00:00 0 7f1dad132000-7f1dad93f000 rw-p 00000000 00:00 0 7f1dad93f000-7f1dad976000 r-xp 00000000 08:01 278421 /usr/lib/x86_64-linux-gnu/libtxc_dxtn_s2tc.so.0.0.0 7f1dad976000-7f1dadb75000 ---p 00037000 08:01 278421 /usr/lib/x86_64-linux-gnu/libtxc_dxtn_s2tc.so.0.0.0 7f1dadb75000-7f1dadb76000 r--p 00036000 08:01 278421 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7f1db3c96000-7f1db3c9e000 r--p 000e5000 08:01 265853 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 7f1db3c9e000-7f1db3ca0000 rw-p 000ed000 08:01 265853 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19 7f1db3ca0000-7f1db3cb5000 rw-p 00000000 00:00 0 7f1db3cb5000-7f1db3cf7000 r-xp 00000000 08:01 299556 /usr/lib/x86_64-linux-gnu/libglut.so.3.9.0 7f1db3cf7000-7f1db3ef7000 ---p 00042000 08:01 299556 /usr/lib/x86_64-linux-gnu/libglut.so.3.9.0 7f1db3ef7000-7f1db3efb000 r--p 00042000 08:01 299556 /usr/lib/x86_64-linux-gnu/libglut.so.3.9.0 7f1db3efb000-7f1db3f00000 rw-p 00046000 08:01 299556 /usr/lib/x86_64-linux-gnu/libglut.so.3.9.0 7f1db3f00000-7f1db3f6c000 r-xp 00000000 08:01 272794 /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1 7f1db3f6c000-7f1db416c000 ---p 0006c000 08:01 272794 /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1 7f1db416c000-7f1db416d000 r--p 0006c000 08:01 272794 /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1 7f1db416d000-7f1db416e000 rw-p 0006d000 08:01 272794 /usr/lib/x86_64-linux-gnu/libGLU.so.1.3.1 7f1db416e000-7f1db41c8000 r-xp 00000000 08:01 270344 /usr/lib/x86_64-linux-gnu/libGL.so.1.2.0 7f1db41c8000-7f1db43c8000 ---p 0005a000 08:01 270344 /usr/lib/x86_64-linux-gnu/libGL.so.1.2.0 7f1db43c8000-7f1db43ca000 r--p 0005a000 08:01 270344 /usr/lib/x86_64-linux-gnu/libGL.so.1.2.0 7f1db43ca000-7f1db43cb000 rw-p 0005c000 08:01 270344 /usr/lib/x86_64-linux-gnu/libGL.so.1.2.0 7f1db43cb000-7f1db43cc000 rw-p 00000000 00:00 0 7f1db43cc000-7f1db444d000 r-xp 00000000 08:01 273938 /usr/lib/x86_64-linux-gnu/libGLEW.so.1.10.0 7f1db444d000-7f1db464d000 ---p 00081000 08:01 273938 /usr/lib/x86_64-linux-gnu/libGLEW.so.1.10.0 7f1db464d000-7f1db4653000 rw-p 00081000 08:01 273938 /usr/lib/x86_64-linux-gnu/libGLEW.so.1.10.0 7f1db4653000-7f1db4658000 rw-p 00000000 00:00 0 7f1db4658000-7f1db46f6000 r-xp 00000000 08:01 270326 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.11.1 7f1db46f6000-7f1db48f5000 ---p 0009e000 08:01 270326 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.11.1 7f1db48f5000-7f1db48fb000 r--p 0009d000 08:01 270326 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.11.1 7f1db48fb000-7f1db48fc000 rw-p 000a3000 08:01 270326 /usr/lib/x86_64-linux-gnu/libfreetype.so.6.11.1 7f1db48fc000-7f1db4922000 r-xp 00000000 08:01 525952 /lib/x86_64-linux-gnu/libpng12.so.0.50.0 7f1db4922000-7f1db4b21000 ---p 00026000 08:01 525952 /lib/x86_64-linux-gnu/libpng12.so.0.50.0 7f1db4b21000-7f1db4b22000 r--p 00025000 08:01 525952 /lib/x86_64-linux-gnu/libpng12.so.0.50.0 7f1db4b22000-7f1db4b23000 rw-p 00026000 08:01 525952 /lib/x86_64-linux-gnu/libpng12.so.0.50.0 7f1db4b23000-7f1db4f84000 r-xp 00000000 08:01 300014 /usr/lib/python2.7/dist-packages/pymol/_cmd.so 7f1db4f84000-7f1db5184000 ---p 00461000 08:01 300014 /usr/lib/python2.7/dist-packages/pymol/_cmd.so 7f1db5184000-7f1db5193000 r--p 00461000 08:01 300014 /usr/lib/python2.7/dist-packages/pymol/_cmd.so 7f1db5193000-7f1db55bd000 rw-p 00470000 08:01 300014 /usr/lib/python2.7/dist-packages/pymol/_cmd.so 7f1db55bd000-7f1db5601000 rw-p 00000000 00:00 0 7f1db5601000-7f1db57c6000 r--p 00000000 08:01 260609 /usr/lib/locale/locale-archive 7f1db57c6000-7f1db5966000 r-xp 00000000 08:01 521248 /lib/x86_64-linux-gnu/libc-2.18.so 7f1db5966000-7f1db5b65000 ---p 001a0000 08:01 521248 /lib/x86_64-linux-gnu/libc-2.18.so 7f1db5b65000-7f1db5b69000 r--p 0019f000 08:01 521248 /lib/x86_64-linux-gnu/libc-2.18.so 7f1db5b69000-7f1db5b6b000 rw-p 001a3000 08:01 521248 /lib/x86_64-linux-gnu/libc-2.18.so 7f1db5b6b000-7f1db5b6f000 rw-p 00000000 00:00 0 7f1db5b6f000-7f1db5c70000 r-xp 00000000 08:01 521245 /lib/x86_64-linux-gnu/libm-2.18.so 7f1db5c70000-7f1db5e70000 ---p 00101000 08:01 521245 /lib/x86_64-linux-gnu/libm-2.18.so 7f1db5e70000-7f1db5e71000 r--p 00101000 08:01 521245 /lib/x86_64-linux-gnu/libm-2.18.so 7f1db5e71000-7f1db5e72000 rw-p 00102000 08:01 521245 /lib/x86_64-linux-gnu/libm-2.18.so 7f1db5e72000-7f1db5e89000 r-xp 00000000 08:01 521435 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f1db5e89000-7f1db6088000 ---p 00017000 08:01 521435 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f1db6088000-7f1db6089000 r--p 00016000 08:01 521435 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f1db6089000-7f1db608a000 rw-p 00017000 08:01 521435 /lib/x86_64-linux-gnu/libz.so.1.2.8 7f1db608a000-7f1db608c000 r-xp 00000000 08:01 521236 /lib/x86_64-linux-gnu/libutil-2.18.so 7f1db608c000-7f1db628b000 ---p 00002000 08:01 521236 /lib/x86_64-linux-gnu/libutil-2.18.so 7f1db628b000-7f1db628c000 r--p 00001000 08:01 521236 /lib/x86_64-linux-gnu/libutil-2.18.so 7f1db628c000-7f1db628d000 rw-p 00002000 08:01 521236 /lib/x86_64-linux-gnu/libutil-2.18.so 7f1db628d000-7f1db6290000 r-xp 00000000 08:01 521240 /lib/x86_64-linux-gnu/libdl-2.18.so 7f1db6290000-7f1db648f000 ---p 00003000 08:01 521240 /lib/x86_64-linux-gnu/libdl-2.18.so 7f1db648f000-7f1db6490000 r--p 00002000 08:01 521240 /lib/x86_64-linux-gnu/libdl-2.18.so 7f1db6490000-7f1db6491000 rw-p 00003000 08:01 521240 /lib/x86_64-linux-gnu/libdl-2.18.so 7f1db6491000-7f1db64a9000 r-xp 00000000 08:01 521234 /lib/x86_64-linux-gnu/libpthread-2.18.so 7f1db64a9000-7f1db66a8000 ---p 00018000 08:01 521234 /lib/x86_64-linux-gnu/libpthread-2.18.so 7f1db66a8000-7f1db66a9000 r--p 00017000 08:01 521234 /lib/x86_64-linux-gnu/libpthread-2.18.so 7f1db66a9000-7f1db66aa000 rw-p 00018000 08:01 521234 /lib/x86_64-linux-gnu/libpthread-2.18.so 7f1db66aa000-7f1db66ae000 rw-p 00000000 00:00 0 7f1db66ae000-7f1db66b2000 r-xp 00000000 08:01 521254 /lib/x86_64-linux-gnu/libSegFault.so 7f1db66b2000-7f1db68b1000 ---p 00004000 08:01 521254 /lib/x86_64-linux-gnu/libSegFault.so 7f1db68b1000-7f1db68b2000 r--p 00003000 08:01 521254 /lib/x86_64-linux-gnu/libSegFault.so 7f1db68b2000-7f1db68b3000 rw-p 00004000 08:01 521254 /lib/x86_64-linux-gnu/libSegFault.so 7f1db68b3000-7f1db68d3000 r-xp 00000000 08:01 521238 /lib/x86_64-linux-gnu/ld-2.18.so 7f1db6902000-7f1db69c2000 rw-p 00000000 00:00 0 7f1db69f3000-7f1db6ab8000 rw-p 00000000 00:00 0 7f1db6acf000-7f1db6ad2000 rw-p 00000000 00:00 0 7f1db6ad2000-7f1db6ad3000 r--p 0001f000 08:01 521238 /lib/x86_64-linux-gnu/ld-2.18.so 7f1db6ad3000-7f1db6ad4000 rw-p 00020000 08:01 521238 /lib/x86_64-linux-gnu/ld-2.18.so 7f1db6ad4000-7f1db6ad5000 rw-p 00000000 00:00 0 7fff4c0d5000-7fff4c0f6000 rw-p 00000000 00:00 0 7fff4c178000-7fff4c17a000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

20 March 2014

567. Testing daisychain slurm script

I'm using stampede.TACC for jobs that need significantly longer than 48 hours to run. Luckily, John Fonner at the Texas Advanced Computing Centre has been kind enough to prepare a SLURM script that circumvents that through daisychaining jobs.

Note that you should under no circumstances do this unless you've been specifically allowed to do so by your cluster manager. 

If you get clearance, you submit the script and it will run in the background and resubmit scripts until the job is done.


To get the daisychain script, do

mkdir ~/tmp
cd ~/tmp
git clone https://github.com/johnfonner/daisychain.git

This will pull the latest version of daisychain.slurm. Rename it to e.g. edited.slurm

General editing of the slurm script:

1.
 Replace all instances of
 
~/.daisychain

with
 
~/daisychain_$baseSlurmJobName

to avoid conflicts when several jobs are running concurrently

2.
To run the script on your own system which you've set up like shown in this post, change

loginNode="login1"

to

loginNode="localhost"

If you're using stampede.TACC, stick to login1.  

3. For gaussian jobs on stampede.TACC  
A.
put

module load gaussian

before

if [ "$thisJobNumber" -eq "1" ]; then

B
Set up your restart job scripts. For example, if the job section of your slurm script looks like this
mkdir $SCRATCH/gaussian_tmp export GAUSS_SCRDIR=$SCRATCH/gaussian_tmp if [ "$thisJobNumber" -eq "1" ]; then #first job echo "Starting First Job:" g09 < freq.g09in > output_$thisJobNumber else #continuation echo "Starting Continuation Job:" g09 < freq_restart.g09in > output_$thisJobNumber fi
with freq.g09in looking like
%nprocshared=16 %rwf=/scratch/0XXXX/XXXX/gaussian_tmp/ajob.rwf %Mem=2000000000 %Chk=/home1/0XXX/XXXX/myjob/ajob.chk #P rpbe1pbe/GEN 5D Freq() SCF=(MaxCycle=256 ) Punch=(MO) Pop=()
with freq.g09in being something along the lines of
%nprocshared=16 %Mem=2000000000 %rwf=/scratch/0XXX/XXXX/gaussian_tmp/ajob.rwf %Chk=/home1/0XXXX/XXXX/myjob/ajob.chk #P restart
(note that the above example is a bit special since it 1) saves the .rwf (which is huge) and 2) is restarting a frequency job. For a simple geoopt job it's enough to restart from the .chk file.

Testing at home
I set up a home system with slurm as shown here: http://verahill.blogspot.com.au/2014/03/565-setting-up-slurm-on-debian-wheezy.html

First edit the daisychain.slurm script as shown above. Note that your slurm script must end with .slurm for the script to recognise it as a slurm script. You can get around this by editing your script and specifying a job script name.

Specifically, change the run time to
#SBATCH -t 00:00:10 # Run time (hh:mm:ss)
comment out the partition name
##SBATCH -p normal
and change the job section to
#-------------------Job Goes Here-------------------------- if [ "$thisJobNumber" -eq "1" ]; then echo "Starting First Job:" sh sleeptest.sh else echo "Starting Continuation Job:" sh sleeptest_2.sh fi #----------------------------------------------------------

Next set up key-based log in for localhost (if you haven't got a keypair, use ssh-keygen:

cat $HOME/.ssh/id_rsa.pub >> $HOME/.ssh/authorized_keys
ssh localhost
  exit

Create two  job files. sleeptest.sh:
echo "first job" date sleep 65 date
and
echo "second job" date sleep 9 echo "Do nothing"

Submit using
sbatch test.slurm

Make sure to change
#SBATCH -J testx          # Job name
for each job so that you can have several running concurrently.

15 March 2014

566. Briefly: Annoying warnings when plotting using gnuplot and octave on wheezy March 2014.

Note: I'm not going to give a proper fix for this, but rather a work-around -- and one which isn't very good at that.

When using gnuplot or plotting in octave on wheezy I keep getting the following warnings.
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-ukai.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 16: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/41-arphic-uming.conf", line 28: Having multiple  in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/64-arphic-uming.conf", line 8: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/64-arphic-uming.conf", line 21: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/64-arphic-uming.conf", line 34: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/64-arphic-uming.conf", line 47: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/65-droid-sans-fonts.conf", line 103: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/65-droid-sans-fonts.conf", line 138: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/90-fonts-baekmuk.conf", line 10: Having multiple values in  isn't supported and may not work as expected
Fontconfig warning: "/etc/fonts/conf.d/90-fonts-baekmuk.conf", line 23: Having multiple values in  isn't supported and may not work as expected

My 'solution' was a bit radical -- I had already set up a system with apt-pinning (http://verahill.blogspot.com.au/2014/03/562-pulling-in-glibc-214-from-testing.html) so I figured that pulling in the fonts from testing couldn't hurt, assuming there were no dependencies to worry about.

So I did:
sudo apt-get install -t testing fonts-arphic-uming
and this worked fine.

The old 41-arphic-uming.conf:
<?xml version="1.0"?>
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<fontconfig>

<!--
  Serif faces
 -->
        <alias>
                <family>AR PL ShanHeiSun Uni</family>
                <family>AR PL ShanHeiSun Uni MBE</family>
                <family>AR PL UMing CN</family>
                <family>AR PL UMing HK</family>
                <family>AR PL UMing TW</family>
                <family>AR PL UMing TW MBE</family>
                <default><family>serif</family></default>
        </alias>
<!--
  Monospace faces
 -->
        <alias>
                <family>AR PL ShanHeiSun Uni</family>
                <family>AR PL ShanHeiSun Uni MBE</family>
                <family>AR PL UMing CN</family>
                <family>AR PL UMing HK</family>
                <family>AR PL UMing TW</family>
                <family>AR PL UMing TW MBE</family>
                <default><family>monospace</family></default>
        </alias>
</fontconfig>
The new 41-arphic-uming.conf:
<?xml version="1.0"?>
<!DOCTYPE fontconfig SYSTEM "fonts.dtd">
<fontconfig>

<!--
  Serif faces
 -->
        <alias>
                <family>AR PL ShanHeiSun Uni</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL ShanHeiSun Uni MBE</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL UMing CN</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL UMing HK</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL UMing TW</family>
                <default><family>serif</family></default>
        </alias>
        <alias>
                <family>AR PL UMing TW MBE</family>
                <default><family>serif</family></default>
        </alias>
<!--
  Monospace faces
 -->
        <alias>
                <family>AR PL ShanHeiSun Uni</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL ShanHeiSun Uni MBE</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL UMing CN</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL UMing HK</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL UMing TW</family>
                <default><family>monospace</family></default>
        </alias>
        <alias>
                <family>AR PL UMing TW MBE</family>
                <default><family>monospace</family></default>
        </alias>
</fontconfig>
It just remained to pull in the rest of the offending fonts:
sudo apt-get install -t testing fonts-arphic-ukai fonts-droid fonts-baekmuk