Render images in nogui mode

[Tom Goddard]

Want to be able to render images in nogui mode on a server that has no display or graphics card.
The PDB requested this for rendering their web site images on a server.

[Tom Goddard]

Begin forwarded message:

From: Ezra Peisach
Subject: Re: Chimera 2.0, mmCIF and biological assemblies.....
Date: June 26, 2015 at 11:55:11 AM PDT
To: Tom Goddard
Cc: Tom Ferrin, Chimera Staff <chimera-staff@…>

Right now - we could benefit from the fast mmCIF parser to aid in our evaluation.

The highest priority moving forward will be the ability to interpret mmCIF assembly information. This is not a show stopper at the moment - but would be best if we do not need to create separate assembly files for generation - but instead could read and parse.

Virus capsids - as you can tell - are from higher order multiscale models... I envision that we would want to keep it.

Eventually - a headless implementation (--nogui) - would be for batch processing....

Ezra

[Tom Goddard]

I tried OSMesa (off-screen Mesa) from Mesa 10.6.2 on a linux system (Ubuntu 15.04) and was able to have Chimera 2 render in --nogui mode both density maps and molecules. I used the OSMesa llvmpipe software renderer that uses llvm to compile shader programs for running on the CPU. The GPU was not used.

[Tom Goddard]

Image rendered with nogui mode and osmesa llvmpipe on Ubuntu 15.04.

[Tom Goddard]

I tried the same OSMesa llvmpipe (mesa 10.6.2) approach on Mac OS 10.10.4 and it crashes in glDrawElementsInstanced() on a memory deallocation (FREE() call) in llvm code as indicated in the following crash dump:

Process: Chimera2 [57020]
Path: /Users/USER/*/Chimera2.app/Contents/bin/Chimera2
Identifier: Chimera2
Version: ???
Code Type: X86-64 (Native)
Parent Process: bash [64539]
Responsible: Emacs-10.7 [64521]
User ID: 501

Date/Time: 2015-07-28 15:26:01.972 -0700
OS Version: Mac OS X 10.10.4 (14E46)
Report Version: 11
Anonymous UUID: ADCA02F2-9A59-6574-CF8F-380125498A20

Time Awake Since Boot: 1200000 seconds

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x00007fe03b887800

VM Regions Near 0x7fe03b887800:

MALLOC_TINY 00007fe03ac00000-00007fe03b000000 [ 4096K] rw-/rwx SM=COW

--> MALLOC_SMALL 00007fe03b000000-00007fe03c000000 [ 16.0M] rw-/rwx SM=PRV

MALLOC_TINY 00007fe03c000000-00007fe03c100000 [ 1024K] rw-/rwx SM=PRV

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff89016c82 kill + 10
1 ??? 000000000000000000 0 + 0
2 libOSMesa.dylib 0x0000000102e3998a llvm_pipeline_generic + 842 (draw_pt_fetch_shade_pipeline_llvm.c:469)
3 libOSMesa.dylib 0x0000000102e39507 llvm_middle_end_run + 87 (draw_pt_fetch_shade_pipeline_llvm.c:503)
4 libOSMesa.dylib 0x0000000102d37e55 vsplit_run_uint + 4629 (draw_pt_vsplit.c:79)
5 libOSMesa.dylib 0x0000000102d2b20b draw_pt_arrays + 459 (draw_pt.c:149)
6 libOSMesa.dylib 0x0000000102d2afd5 draw_vbo + 1045 (draw_pt.c:547)
7 libOSMesa.dylib 0x0000000102e947d1 llvmpipe_draw_vbo + 513 (lp_draw_arrays.c:137)
8 libOSMesa.dylib 0x0000000102bc3340 st_draw_vbo + 800 (st_draw.c:257)
9 libOSMesa.dylib 0x0000000102b928be vbo_exec_DrawElementsInstanced + 254 (vbo_exec_array.c:1173)
10 _ctypes.so 0x0000000101bac697 ffi_call_unix64 + 79 (darwin64.S:79)
11 _ctypes.so 0x0000000101bacef8 ffi_call + 872 (x86-ffi64.c:581)
12 _ctypes.so 0x0000000101ba805b _ctypes_callproc + 891 (callproc.c:811)
13 _ctypes.so 0x0000000101ba22f1 PyCFuncPtr_call + 1057 (_ctypes.c:3848)
14 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
15 org.python.python 0x0000000100da8455 slot_tp_call + 117 (typeobject.c:5962)
16 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
17 org.python.python 0x0000000100e0a01f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
18 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
19 org.python.python 0x0000000100d7913d function_call + 381 (funcobject.c:632)
20 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
21 org.python.python 0x0000000100d671bd method_call + 141 (classobject.c:347)
22 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
23 org.python.python 0x0000000100da8455 slot_tp_call + 117 (typeobject.c:5962)
24 wrapper.so 0x000000010533f479 pyx_pw_17OpenGL_accelerate_7wrapper_7Wrapper_3call + 1161 (wrapper.c:11473)
25 latebind.so 0x000000010536b2bf pyx_pw_17OpenGL_accelerate_8latebind_8LateBind_7call + 511 (latebind.c:1680)
26 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
27 org.python.python 0x0000000100e095ae PyEval_EvalFrameEx + 20958 (ceval.c:4466)
28 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
29 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
30 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
31 org.python.python 0x0000000100e0cfc2 fast_function + 210 (ceval.c:4334)
32 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
33 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
34 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
35 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
36 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
37 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
38 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
39 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
40 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
41 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
42 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
43 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
44 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
45 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
46 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
47 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
48 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
49 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
50 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
51 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
52 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
53 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
54 org.python.python 0x0000000100e0cfc2 fast_function + 210 (ceval.c:4334)
55 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
56 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
57 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
58 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
59 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
60 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
61 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
62 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
63 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
64 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
65 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
66 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
67 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
68 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
69 org.python.python 0x0000000100d7913d function_call + 381 (funcobject.c:632)
70 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
71 org.python.python 0x0000000100e0a01f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
72 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
73 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
74 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
75 org.python.python 0x0000000100e0cfc2 fast_function + 210 (ceval.c:4334)
76 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
77 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
78 org.python.python 0x0000000100d7913d function_call + 381 (funcobject.c:632)
79 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
80 org.python.python 0x0000000100e0a01f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
81 org.python.python 0x0000000100e0cfc2 fast_function + 210 (ceval.c:4334)
82 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
83 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
84 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
85 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
86 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
87 org.python.python 0x0000000100e0384f PyEval_EvalCode + 63 (ceval.c:775)
88 org.python.python 0x0000000100e23ab5 PyImport_ImportFrozenModuleObject + 469 (import.c:869)
89 org.python.python 0x0000000100e23ba2 PyImport_ImportFrozenModule + 34 (import.c:1291)
90 org.python.python 0x0000000100e1d45e Py_FrozenMain + 430 (frozenmain.c:84)
91 libdyld.dylib 0x00007fff831795c9 start + 1

Thread 1:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libOSMesa.dylib 0x0000000102e9647b thread_function + 235 (os_thread.h:258)
2 libOSMesa.dylib 0x0000000102e96629 impl_thrd_routine + 25 (threads_posix.h:87)
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 2:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libOSMesa.dylib 0x0000000102e9647b thread_function + 235 (os_thread.h:258)
2 libOSMesa.dylib 0x0000000102e96629 impl_thrd_routine + 25 (threads_posix.h:87)
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 3:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libOSMesa.dylib 0x0000000102e9647b thread_function + 235 (os_thread.h:258)
2 libOSMesa.dylib 0x0000000102e96629 impl_thrd_routine + 25 (threads_posix.h:87)
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 4:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libOSMesa.dylib 0x0000000102e9647b thread_function + 235 (os_thread.h:258)
2 libOSMesa.dylib 0x0000000102e96629 impl_thrd_routine + 25 (threads_posix.h:87)
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 5:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libOSMesa.dylib 0x0000000102e9647b thread_function + 235 (os_thread.h:258)
2 libOSMesa.dylib 0x0000000102e96629 impl_thrd_routine + 25 (threads_posix.h:87)
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 6:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libOSMesa.dylib 0x0000000102e9647b thread_function + 235 (os_thread.h:258)
2 libOSMesa.dylib 0x0000000102e96629 impl_thrd_routine + 25 (threads_posix.h:87)
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 7:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libOSMesa.dylib 0x0000000102e9647b thread_function + 235 (os_thread.h:258)
2 libOSMesa.dylib 0x0000000102e96629 impl_thrd_routine + 25 (threads_posix.h:87)
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 8:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 libOSMesa.dylib 0x0000000102e9647b thread_function + 235 (os_thread.h:258)
2 libOSMesa.dylib 0x0000000102e96629 impl_thrd_routine + 25 (threads_posix.h:87)
3 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
4 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
5 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 9:: Dispatch queue: com.apple.libdispatch-manager
0 libsystem_kernel.dylib 0x00007fff89018232 kevent64 + 10
1 libdispatch.dylib 0x00007fff87692a6a _dispatch_mgr_thread + 52

Thread 10:

Thread 11:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 org.python.python 0x0000000100e468b5 PyThread_acquire_lock_timed + 293 (thread_pthread.h:500)
2 org.python.python 0x0000000100e4cdaf acquire_timed + 143 (_threadmodule.c:71)
3 org.python.python 0x0000000100e4cf8c lock_PyThread_acquire_lock + 300 (_threadmodule.c:139)
4 org.python.python 0x0000000100e09913 PyEval_EvalFrameEx + 21827 (ceval.c:4237)
5 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
6 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
7 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
8 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
9 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
10 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
11 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
12 org.python.python 0x0000000100d7913d function_call + 381 (funcobject.c:632)
13 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
14 org.python.python 0x0000000100e0a01f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
15 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
16 org.python.python 0x0000000100d7913d function_call + 381 (funcobject.c:632)
17 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
18 org.python.python 0x0000000100e0a01f PyEval_EvalFrameEx + 23631 (ceval.c:4561)
19 org.python.python 0x0000000100e0cfc2 fast_function + 210 (ceval.c:4334)
20 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
21 org.python.python 0x0000000100e0cfc2 fast_function + 210 (ceval.c:4334)
22 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
23 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
24 org.python.python 0x0000000100d7913d function_call + 381 (funcobject.c:632)
25 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
26 org.python.python 0x0000000100d671bd method_call + 141 (classobject.c:347)
27 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
28 org.python.python 0x0000000100e0c65d PyEval_CallObjectWithKeywords + 93 (ceval.c:4114)
29 org.python.python 0x0000000100e4c756 t_bootstrap + 70 (_threadmodule.c:1001)
30 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
31 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
32 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 12:
0 libsystem_kernel.dylib 0x00007fff89017136 psynch_cvwait + 10
1 org.python.python 0x0000000100e46894 PyThread_acquire_lock_timed + 260 (thread_pthread.h:492)
2 org.python.python 0x0000000100e4cdaf acquire_timed + 143 (_threadmodule.c:71)
3 org.python.python 0x0000000100e4cf8c lock_PyThread_acquire_lock + 300 (_threadmodule.c:139)
4 org.python.python 0x0000000100e09913 PyEval_EvalFrameEx + 21827 (ceval.c:4237)
5 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
6 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
7 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
8 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
9 org.python.python 0x0000000100e0d02c fast_function + 316 (ceval.c:4348)
10 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
11 org.python.python 0x0000000100e0cfc2 fast_function + 210 (ceval.c:4334)
12 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
13 org.python.python 0x0000000100e0cfc2 fast_function + 210 (ceval.c:4334)
14 org.python.python 0x0000000100e09314 PyEval_EvalFrameEx + 20292 (ceval.c:4262)
15 org.python.python 0x0000000100e04267 PyEval_EvalCodeEx + 2567 (ceval.c:3588)
16 org.python.python 0x0000000100d7913d function_call + 381 (funcobject.c:632)
17 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
18 org.python.python 0x0000000100d671bd method_call + 141 (classobject.c:347)
19 org.python.python 0x0000000100d53bc7 PyObject_Call + 103 (abstract.c:2040)
20 org.python.python 0x0000000100e0c65d PyEval_CallObjectWithKeywords + 93 (ceval.c:4114)
21 org.python.python 0x0000000100e4c756 t_bootstrap + 70 (_threadmodule.c:1001)
22 libsystem_pthread.dylib 0x00007fff8b89a268 _pthread_body + 131
23 libsystem_pthread.dylib 0x00007fff8b89a1e5 _pthread_start + 176
24 libsystem_pthread.dylib 0x00007fff8b89841d thread_start + 13

Thread 0 crashed with X86 Thread State (64-bit):

rax: 0x0000000000000000 rbx: 0x00000001010f4f48 rcx: 0x00000001010f4aa8 rdx: 0x0000000000000000
rdi: 0x000000000000debc rsi: 0x000000000000000a rbp: 0x00000001010f4ab0 rsp: 0x00000001010f4aa8

r8: 0x00000001010f4f48 r9: 0x00007fe03ba5d800 r10: 0x00007fff89018c22 r11: 0x0000000000000202

r12: 0x000000000000011a r13: 0x00007fe03ba5cc00 r14: 0x0000000000000000 r15: 0x00007fff5eebc0a0
rip: 0x00007fff89016c82 rfl: 0x0000000000000202 cr2: 0x00000001100f9000

Logical CPU: 0
Error Code: 0x02000025
Trap Number: 133

Binary Images:

0x100d40000 - 0x100d40ff7 +edu.ucsf.cgl.Chimera2 (2.0.0 - 2.0.0.0) <73F8A8A6-F58F-3A9D-8AD0-972177C7A943> /Users/USER/*/Chimera2.app/Contents/MacOS/Chimera2
0x100d47000 - 0x100ed6ff7 +org.python.python (3.4.3, [c] 2001-2015 Python Software Foundation. - 3.4.3) <B05216B6-F925-3443-8EDD-E303D42E94A4> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/Python
0x101286000 - 0x101288fff +time.so (0) <307B7F4F-645D-3C3D-BFEF-0A5C4F6D390A> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/time.so
0x1012d0000 - 0x1012d1fff +_heapq.so (0) <C9A206E4-A401-3B7E-8740-A5BAE8839184> /Users/USER/*/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/lib-dynload/_heapq.so
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0x7fff8b897000 - 0x7fff8b8a0fff libsystem_pthread.dylib (105.10.1) <3103AA7F-3BAE-3673-9649-47FFD7E15C97> /usr/lib/system/libsystem_pthread.dylib
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0x7fff8bda0000 - 0x7fff8bda0fff com.apple.Accelerate (1.10 - Accelerate 1.10) <F1B96A61-7E4B-31BD-A35B-BA7EF1F16EF4> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
0x7fff8c1ae000 - 0x7fff8c1b4fff libsystem_trace.dylib (72.20.1) <840F5301-B55A-3078-90B9-FEFFD6CD741A> /usr/lib/system/libsystem_trace.dylib
0x7fff8ca4e000 - 0x7fff8ca94ff7 libauto.dylib (186) <A260789B-D4D8-316A-9490-254767B8A5F1> /usr/lib/libauto.dylib
0x7fff8cab3000 - 0x7fff8cab4ff7 libsystem_blocks.dylib (65) <9615D10A-FCA7-3BE4-AA1A-1B195DACE1A1> /usr/lib/system/libsystem_blocks.dylib
0x7fff8cce0000 - 0x7fff8cd18fff libsystem_network.dylib (412.20.3) <6105C134-6722-3C0A-A4CE-5E1261E2E1CC> /usr/lib/system/libsystem_network.dylib
0x7fff8cda8000 - 0x7fff8ce21fe7 libcorecrypto.dylib (233.30.1) <5779FFA0-4D9A-3AD4-B7F2-618227621DC8> /usr/lib/system/libcorecrypto.dylib
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0x7fff8eb47000 - 0x7fff8eedfff7 com.apple.CoreFoundation (6.9 - 1153.18) <5C0892B8-9691-341F-9279-CA3A74D59AA0> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
0x7fff8eef3000 - 0x7fff8f0d8ff7 libicucore.A.dylib (531.48) <3CD34752-B1F9-31D2-865D-B5B0F0BE3111> /usr/lib/libicucore.A.dylib
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0x7fff919f4000 - 0x7fff91e47fc7 com.apple.vImage (8.0 - 8.0) <33BE7B31-72DB-3364-B37E-C322A32748C5> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage

External Modification Summary:

Calls made by other processes targeting this process:

task_for_pid: 0
thread_create: 0
thread_set_state: 0

Calls made by this process:

task_for_pid: 0
thread_create: 0
thread_set_state: 0

Calls made by all processes on this machine:

task_for_pid: 363843
thread_create: 0
thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=143.8M resident=82.3M(57%) swapped_out_or_unallocated=61.5M(43%)
Writable regions: Total=175.8M written=55.8M(32%) resident=65.1M(37%) swapped_out=0K(0%) unallocated=110.7M(63%)

REGION TYPE VIRTUAL
=========== =======
Dispatch continuations 16.0M
Kernel Alloc Once 4K
MALLOC 131.8M
MALLOC (admin) 16K
MALLOC_LARGE (reserved) 1152K reserved VM address space (unallocated)
STACK GUARD 44K
Stack 78.2M
Stack (reserved) 520K reserved VM address space (unallocated)
VM_ALLOCATE 60K
DATA 5696K
LINKEDIT 87.6M
TEXT 56.2M
UNICODE 552K
shared memory 24K
=========== =======
TOTAL 377.6M
TOTAL, minus reserved VM space 376.0M

[Tom Goddard]

For server rendering probably Linux is the only important platform, so I'm giving up on Mac OSMesa for now.

[Tom Goddard]

Another approach besides OSMesa for server rendering would be to use EGL. Current Linux distributions will still require an X server running to use EGL because only the X server talks to the graphics drivers, not the linux kernel. But an X server can be run on a server that has no display using an appropriate X config file to create a virtual display. This approach has the advantage that hardware acceleration could be used, for example mesa talking to an Intel CPU/GPU. This would give faster rendering. It may also give more robust rendering than an osmesa all software approach since the latter is probably much more rarely used than standard graphics drivers which EGL would make use of. Another advantage is we would not have to build and include OSMesa in our Chimera distribution. The drawback is that it is harder for the user to setup server rendering, since it would be necessary to start an X server with virtual display.

[Tom Goddard]

I attempted putting in code that tries to use OSMesa when Chimera is started in --nogui mode, and then if it is not found continue without it. Unfortunately this does not work. The only way to tell PyOpenGL to use osmesa is to set an environment variable PYOPENGL_PLATFORM=osmesa. This can be done in python code using os.environ before importing PyOpenGL. The trouble is that if the osmesa library is not fail it raises an error and PyOpenGL is left in an unusable state.

I think the solution here is to only attempt to use osmesa on platforms where Chimera includes the library. I'm currently not including osmesa and llvm libraries in Chimera.

[Tom Goddard]

Mac OS does not support EGL.

[Tom Goddard]

Getting PyOpenGL to find libOSMesa.so on Linux requires patching PyOpenGL to find the library installed with Chimera. It only tries to look in standard system locations and ignores LD_LIBRARY_PATH as described in this bug report.

​https://bugs.python.org/issue9998

PyOpenGL also has to be patched to make osmesa work without getting an unhashable type for the OpenGL context.

[Tom Goddard]

I added mesa, llvm, and pkg-config to prereqs to build osmesa. The mesa build is configured to only make osmesa with the llvmpipe software rasterizer. It requires llvm (just-in-time compiler) and pkg-config. These are only built on Linux because with Mesa 10.6.3 osmesa crashes in glDrawElementsInstanced() on Mac. Unfortunately this adds almost an hour to the compile time of Chimera (36 minutes for llvm, 18 minutes for mesa) using one core on our vmware plato build machine.

I also patched PyOpenGL to find the OSMesa library and fix an unhashable type error.

I tested on our build machine plato-vmware.cgl.ucsf.edu:8964 and it correctly saved a molecule image (1a0n) with full lighting.

[Tom Goddard]

The test was on 1aon (~60,000 atoms) and took about 1 minute to render -- quite slow.

[Tom Goddard]

Using soft lighting I rendered images for all assemblies for PDB codes with middle two letters aa, 126 mmCIF files producing 168 PNG images. On my office iMac with Nvidia Geforce 680MX graphcis this took 60 seconds in GUI mode. On Intel HD 6000 graphics on my home linux box it took 97 seconds in GUI mode. On the same linux machine using nogui mode with osmesa llvmpipe rendering it took 2370 seconds. So it is about 40 times slower than rendering with a decent Nvidia graphics card.

The entire PDB would take about half a day to render all assemblies with the Nvidia graphics in GUI mode, but 20 days to render in nogui mode.

Chimera 2 memory use after rendering all images in nogui mode was 170 Mbytes.

The nogui rendered images looked as good as the gui images, gauged by eye looking at montage.

[Tom Goddard]

On Mac 10.10.5 with GeForce GTX 680MX graphics (descartes.cgl.ucsf.edu) rendering the mmCIF/j4 directory images produces incorrect images starting at 3j4u a large virus capsid. The next 15 images for several cif files simply alternate between the previous two images not rendering any new graphics. Then it recovers and starts rendering correctly. It is surprising that the graphics driver fails but doesn't crash.

On Linux Ubuntu 15.04 with Intel HD 6000 graphics (beetracker) rendering mmCIF/j4 works correctly, taking 310 seconds to render 214 images for 117 mmcif files. It also renders all images correctly in nogui mode, taking 19115 seconds (62 times longer). In nogui (cpu rendering with osmesa llvmpipe) a couple images take over an hour to render each (3j4u_1, 1 hour 16 minutes, 3j40_1, 1 hour 13 minutes) while each takes about 60 seconds in gui mode using the intel graphics.

[Tom Goddard]

Working on Linux using OSMesa (off-screen mesa) with LLVM driver.