Task 38603231
| Name | p38_A12_A33_r0_1-QUICO_ATM_GAFF2_NAGL_p38-0-6-RND1972_4 |
| Workunit | 31553235 |
| Created | 10 Apr 2026, 14:20:27 UTC |
| Sent | 10 Apr 2026, 14:20:33 UTC |
| Report deadline | 15 Apr 2026, 14:20:33 UTC |
| Received | 11 Apr 2026, 8:55:15 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 649261 |
| Run time | 1 min 44 sec |
| CPU time | 19 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 9,299.48 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 446.75 MB |
| Peak swap size | 1.69 GB |
| Peak disk usage | 1.44 GB |
Stderr output
<core_client_version>8.0.4</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-04-10 16:32:58 (16382): wrapper (8.1.26018): starting
2026-04-10 16:33:23 (16382): wrapper: running bin/python (bin/conda-unpack)
2026-04-10 16:33:23 (16382): wrapper: created child process 16386
2026-04-10 16:33:24 (16382): bin/python exited; CPU time 0.191491
2026-04-10 16:33:24 (16382): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-10 16:33:24 (16382): wrapper: created child process 16387
2026-04-10 16:33:27 (16382): bin/tar exited; CPU time 2.574857
2026-04-10 16:33:27 (16382): wrapper: running bin/bash (run.sh)
2026-04-10 16:33:27 (16382): wrapper: created child process 16389
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/BOINC/slots/0/bin
+++ dirname /BOINC/slots/0/bin
++ local full_path_env=/BOINC/slots/0
+++ basename /BOINC/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/BOINC/slots/0
++ CONDA_PREFIX=/BOINC/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/BOINC/slots/0/etc/conda/activate.d
++ '[' -d /BOINC/slots/0/etc/conda/activate.d ']'
+ export PATH=/BOINC/slots/0:/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/BOINC/slots/0:/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/BOINC/slots/0/tmp
+ TMP=/BOINC/slots/0/tmp
+ mkdir -p /BOINC/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/BOINC/slots/0/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample does not exist.'
+ echo 'Install ATM and deps'
+ python -m pip list
+ python -m pip install pyaml -v
+ python -m pip install --no-dependencies atom-openmm -v
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A12_A33_input.yaml
+ python bin/rbfe_production QB_A12_A33_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
SIGSEGV: segmentation violation
Stack trace (13 frames):
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x42c050]
/lib64/libc.so.6(+0x41090) [0x7f5360bce090]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x463138]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x45f5d5]
/lib64/libc.so.6(+0x41090) [0x7f5360bce090]
/lib64/libc.so.6(clock_nanosleep+0x67) [0x7f5360c69955]
/lib64/libc.so.6(nanosleep+0x19) [0x7f5360c74ee7]
/lib64/libc.so.6(usleep+0x4b) [0x7f5360c9fbb9]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x4398c2]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x40b2e5]
/lib64/libc.so.6(+0x2a340) [0x7f5360bb7340]
/lib64/libc.so.6(__libc_start_main+0x8b) [0x7f5360bb7409]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x407cc5]
Exiting...
/BOINC/slots/0/lib/python3.11/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 3 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '
2026-04-11 09:59:22 (2801): wrapper (8.1.26018): starting
2026-04-11 09:59:51 (2801): wrapper: running bin/bash (run.sh)
2026-04-11 09:59:51 (2801): wrapper: created child process 3505
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/BOINC/slots/0/bin
+++ dirname /BOINC/slots/0/bin
++ local full_path_env=/BOINC/slots/0
+++ basename /BOINC/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/BOINC/slots/0
++ CONDA_PREFIX=/BOINC/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/BOINC/slots/0/etc/conda/activate.d
++ '[' -d /BOINC/slots/0/etc/conda/activate.d ']'
+ export PATH=/BOINC/slots/0:/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/BOINC/slots/0:/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/BOINC/slots/0/tmp
+ TMP=/BOINC/slots/0/tmp
+ mkdir -p /BOINC/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/BOINC/slots/0/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A12_A33_input.yaml
+ python bin/rbfe_production QB_A12_A33_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/BOINC/slots/0/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/BOINC/slots/0/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 29, in rbfe_production
rx = openmm_job_RBFE(
^^^^^^^^^^^^^^^^
File "/BOINC/slots/0/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 443, in __init__
self.openmm_workers.append(ommworkercls(self.basename, ommsys, self.keywords, node_info = node, compute = True, logger = self.logger))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/BOINC/slots/0/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 53, in __init__
self.start_worker()
File "/BOINC/slots/0/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 444, in start_worker
self._openmm_worker_makecontext()
File "/BOINC/slots/0/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 229, in _openmm_worker_makecontext
self.platform = Platform.getPlatformByName(self.platform_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/BOINC/slots/0/lib/python3.11/site-packages/openmm/openmm.py", line 9567, in getPlatformByName
return _openmm.Platform_getPlatformByName(name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: There is no registered Platform called "CUDA"
2026-04-11 10:00:36 (2801): bin/bash exited; CPU time 19.973181
2026-04-11 10:00:36 (2801): app exit status: 0x1
2026-04-11 10:00:36 (2801): called boinc_finish(195)
</stderr_txt>
]]>
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