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
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7f1dac4b0000-7f1dacf30000 rwxp 00000000 00:00 0
7f1dacf30000-7f1dad031000 rw-p 00000000 00:00 0
7f1dad032000-7f1dad132000 rwxp 00000000 00:00 0
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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 /usr/lib/x86_64-linux-gnu/libtxc_dxtn_s2tc.so.0.0.0
7f1dadb76000-7f1dadb77000 rw-p 00037000 08:01 278421 /usr/lib/x86_64-linux-gnu/libtxc_dxtn_s2tc.so.0.0.0
7f1dadb77000-7f1daf0ac000 r-xp 00000000 08:01 270279 /usr/lib/x86_64-linux-gnu/libLLVM-3.3.so.1
7f1daf0ac000-7f1daf1c3000 rw-p 01535000 08:01 270279 /usr/lib/x86_64-linux-gnu/libLLVM-3.3.so.1
7f1daf1c3000-7f1daf1d5000 rw-p 00000000 00:00 0
7f1daf1d5000-7f1daf1dc000 r-xp 00000000 08:01 265205 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.1
7f1daf1dc000-7f1daf3db000 ---p 00007000 08:01 265205 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.1
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7f1daf3dc000-7f1daf3dd000 rw-p 00007000 08:01 265205 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.1
7f1daf3dd000-7f1daf404000 r-xp 00000000 08:01 521410 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f1daf404000-7f1daf604000 ---p 00027000 08:01 521410 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f1daf604000-7f1daf606000 r--p 00027000 08:01 521410 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f1daf606000-7f1daf607000 rw-p 00029000 08:01 521410 /lib/x86_64-linux-gnu/libexpat.so.1.6.0
7f1daf607000-7f1dafb63000 r-xp 00000000 08:01 401825 /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
7f1dafb63000-7f1dafd63000 ---p 0055c000 08:01 401825 /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
7f1dafd63000-7f1dafd80000 r--p 0055c000 08:01 401825 /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
7f1dafd80000-7f1dafd8a000 rw-p 00579000 08:01 401825 /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
7f1dafd8a000-7f1daffb0000 rw-p 00000000 00:00 0
7f1daffb7000-7f1db03b1000 rw-p 00000000 00:00 0
7f1db03b1000-7f1db0575000 r-xp 00000000 08:01 265863 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7f1db0575000-7f1db0775000 ---p 001c4000 08:01 265863 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7f1db0775000-7f1db0790000 r--p 001c4000 08:01 265863 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7f1db0790000-7f1db079f000 rw-p 001df000 08:01 265863 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0
7f1db079f000-7f1db07a3000 rw-p 00000000 00:00 0
7f1db07a3000-7f1db07f8000 r-xp 00000000 08:01 265878 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f1db07f8000-7f1db09f8000 ---p 00055000 08:01 265878 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f1db09f8000-7f1db09fb000 r--p 00055000 08:01 265878 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f1db09fb000-7f1db0a02000 rw-p 00058000 08:01 265878 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0
7f1db0a02000-7f1db0a06000 r-xp 00000000 08:01 274397 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7f1db0a06000-7f1db0c05000 ---p 00004000 08:01 274397 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7f1db0c05000-7f1db0c06000 r--p 00003000 08:01 274397 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7f1db0c06000-7f1db0c07000 rw-p 00004000 08:01 274397 /usr/lib/python2.7/lib-dynload/_hashlib.x86_64-linux-gnu.so
7f1db0c07000-7f1db0d08000 rw-p 00000000 00:00 0
7f1db0d08000-7f1db0d0c000 r-xp 00000000 08:01 521455 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f1db0d0c000-7f1db0f0b000 ---p 00004000 08:01 521455 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f1db0f0b000-7f1db0f0c000 r--p 00003000 08:01 521455 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f1db0f0c000-7f1db0f0d000 rw-p 00004000 08:01 521455 /lib/x86_64-linux-gnu/libuuid.so.1.3.0
7f1db0f0d000-7f1db0f24000 r-xp 00000000 08:01 271415 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f1db0f24000-7f1db1123000 ---p 00017000 08:01 271415 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f1db1123000-7f1db1125000 rw-p 00016000 08:01 271415 /usr/lib/x86_64-linux-gnu/libICE.so.6.3.0
7f1db1125000-7f1db1128000 rw-p 00000000 00:00 0
7f1db1128000-7f1db112f000 r-xp 00000000 08:01 271417 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f1db112f000-7f1db132e000 ---p 00007000 08:01 271417 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f1db132e000-7f1db132f000 rw-p 00006000 08:01 271417 /usr/lib/x86_64-linux-gnu/libSM.so.6.0.1
7f1db132f000-7f1db1334000 r-xp 00000000 08:01 270065 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f1db1334000-7f1db1533000 ---p 00005000 08:01 270065 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f1db1533000-7f1db1534000 rw-p 00004000 08:01 270065 /usr/lib/x86_64-linux-gnu/libXdmcp.so.6.0.0
7f1db1534000-7f1db1537000 r-xp 00000000 08:01 270059 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f1db1537000-7f1db1736000 ---p 00003000 08:01 270059 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
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7f1db1737000-7f1db1738000 rw-p 00003000 08:01 270059 /usr/lib/x86_64-linux-gnu/libXau.so.6.0.0
7f1db1738000-7f1db1797000 r-xp 00000000 08:01 271512 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f1db1797000-7f1db1997000 ---p 0005f000 08:01 271512 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f1db1997000-7f1db1998000 r--p 0005f000 08:01 271512 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f1db1998000-7f1db199d000 rw-p 00060000 08:01 271512 /usr/lib/x86_64-linux-gnu/libXt.so.6.0.0
7f1db199d000-7f1db199e000 rw-p 00000000 00:00 0
7f1db199e000-7f1db19a5000 r-xp 00000000 08:01 521242 /lib/x86_64-linux-gnu/librt-2.18.so
7f1db19a5000-7f1db1ba4000 ---p 00007000 08:01 521242 /lib/x86_64-linux-gnu/librt-2.18.so
7f1db1ba4000-7f1db1ba5000 r--p 00006000 08:01 521242 /lib/x86_64-linux-gnu/librt-2.18.so
7f1db1ba5000-7f1db1ba6000 rw-p 00007000 08:01 521242 /lib/x86_64-linux-gnu/librt-2.18.so
7f1db1ba6000-7f1db1bb1000 r-xp 00000000 08:01 270264 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f1db1bb1000-7f1db1db0000 ---p 0000b000 08:01 270264 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f1db1db0000-7f1db1db1000 r--p 0000a000 08:01 270264 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f1db1db1000-7f1db1db2000 rw-p 0000b000 08:01 270264 /usr/lib/x86_64-linux-gnu/libdrm.so.2.4.0
7f1db1db2000-7f1db1db7000 r-xp 00000000 08:01 270342 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f1db1db7000-7f1db1fb6000 ---p 00005000 08:01 270342 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f1db1fb6000-7f1db1fb7000 r--p 00004000 08:01 270342 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f1db1fb7000-7f1db1fb8000 rw-p 00005000 08:01 270342 /usr/lib/x86_64-linux-gnu/libXxf86vm.so.1.0.0
7f1db1fb8000-7f1db1fd6000 r-xp 00000000 08:01 270070 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f1db1fd6000-7f1db21d5000 ---p 0001e000 08:01 270070 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f1db21d5000-7f1db21d6000 r--p 0001d000 08:01 270070 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f1db21d6000-7f1db21d7000 rw-p 0001e000 08:01 270070 /usr/lib/x86_64-linux-gnu/libxcb.so.1.1.0
7f1db21d7000-7f1db21da000 r-xp 00000000 08:01 270293 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f1db21da000-7f1db23da000 ---p 00003000 08:01 270293 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f1db23da000-7f1db23db000 r--p 00003000 08:01 270293 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f1db23db000-7f1db23dc000 rw-p 00004000 08:01 270293 /usr/lib/x86_64-linux-gnu/libxcb-dri2.so.0.0.0
7f1db23dc000-7f1db23f1000 r-xp 00000000 08:01 270334 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f1db23f1000-7f1db25f0000 ---p 00015000 08:01 270334 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f1db25f0000-7f1db25f2000 r--p 00014000 08:01 270334 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f1db25f2000-7f1db25f3000 rw-p 00016000 08:01 270334 /usr/lib/x86_64-linux-gnu/libxcb-glx.so.0.0.0
7f1db25f3000-7f1db25f4000 r-xp 00000000 08:01 270305 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f1db25f4000-7f1db27f3000 ---p 00001000 08:01 270305 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f1db27f3000-7f1db27f4000 r--p 00000000 08:01 270305 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f1db27f4000-7f1db27f5000 rw-p 00001000 08:01 270305 /usr/lib/x86_64-linux-gnu/libX11-xcb.so.1.0.0
7f1db27f5000-7f1db27fa000 r-xp 00000000 08:01 270336 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f1db27fa000-7f1db29f9000 ---p 00005000 08:01 270336 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f1db29f9000-7f1db29fa000 r--p 00004000 08:01 270336 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f1db29fa000-7f1db29fb000 rw-p 00005000 08:01 270336 /usr/lib/x86_64-linux-gnu/libXfixes.so.3.1.0
7f1db29fb000-7f1db29fd000 r-xp 00000000 08:01 270338 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f1db29fd000-7f1db2bfc000 ---p 00002000 08:01 270338 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f1db2bfc000-7f1db2bfd000 r--p 00001000 08:01 270338 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f1db2bfd000-7f1db2bfe000 rw-p 00002000 08:01 270338 /usr/lib/x86_64-linux-gnu/libXdamage.so.1.1.0
7f1db2bfe000-7f1db2c1f000 r-xp 00000000 08:01 270266 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f1db2c1f000-7f1db2e1f000 ---p 00021000 08:01 270266 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f1db2e1f000-7f1db2e22000 r--p 00021000 08:01 270266 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f1db2e22000-7f1db2e23000 rw-p 00024000 08:01 270266 /usr/lib/x86_64-linux-gnu/libglapi.so.0.0.0
7f1db2e23000-7f1db2e24000 rw-p 00000000 00:00 0
7f1db2e24000-7f1db2f59000 r-xp 00000000 08:01 270078 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f1db2f59000-7f1db3159000 ---p 00135000 08:01 270078 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f1db3159000-7f1db315a000 r--p 00135000 08:01 270078 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f1db315a000-7f1db315f000 rw-p 00136000 08:01 270078 /usr/lib/x86_64-linux-gnu/libX11.so.6.3.0
7f1db315f000-7f1db3170000 r-xp 00000000 08:01 270340 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f1db3170000-7f1db336f000 ---p 00011000 08:01 270340 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f1db336f000-7f1db3370000 r--p 00010000 08:01 270340 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f1db3370000-7f1db3371000 rw-p 00011000 08:01 270340 /usr/lib/x86_64-linux-gnu/libXext.so.6.4.0
7f1db3371000-7f1db3380000 r-xp 00000000 08:01 270932 /usr/lib/x86_64-linux-gnu/libXi.so.6.1.0
7f1db3380000-7f1db357f000 ---p 0000f000 08:01 270932 /usr/lib/x86_64-linux-gnu/libXi.so.6.1.0
7f1db357f000-7f1db3580000 r--p 0000e000 08:01 270932 /usr/lib/x86_64-linux-gnu/libXi.so.6.1.0
7f1db3580000-7f1db3581000 rw-p 0000f000 08:01 270932 /usr/lib/x86_64-linux-gnu/libXi.so.6.1.0
7f1db3581000-7f1db3599000 r-xp 00000000 08:01 272833 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f1db3599000-7f1db3799000 ---p 00018000 08:01 272833 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f1db3799000-7f1db379b000 rw-p 00018000 08:01 272833 /usr/lib/x86_64-linux-gnu/libXmu.so.6.2.0
7f1db379b000-7f1db37b0000 r-xp 00000000 08:01 521230 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1db37b0000-7f1db39b0000 ---p 00015000 08:01 521230 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1db39b0000-7f1db39b1000 rw-p 00015000 08:01 521230 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f1db39b1000-7f1db3a96000 r-xp 00000000 08:01 265853 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f1db3a96000-7f1db3c96000 ---p 000e5000 08:01 265853 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
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]

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.

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