diekhans
commented
4 years ago Look at the document ion on the current LSF, it does seem that the -a is a newer option.
You would have to modify the Toil LSF batch system to handle the older version. Support for HPC batch systems is difficult, do to all the variation in both software and configuration. We do not have the funding to support all of them.
May I suggest asking your admins if they would upgrade or find a different compute facility.
YPGG1234 notifications@github.com writes:
Hi , I submit my jobs to LSF system with commad
cactus --disableCaching --workDir /tmp --binariesMode local --batchSystem LSF jobStore cfg test.halBut I got:
Root logger is at level 'INFO', 'toil' logger at level 'INFO'. Root logger is at level 'INFO', 'toil' logger at level 'INFO'. The workflow ID is: '7fd37406-ef95-403f-b4c1-4ae2ab6d0fe6' No branch length for test1: setting to 1 No branch length for test2: setting to 1 Using config from path /home/cactus/lib/python2.7/site-packages/cactus/cactus_progressive_config.xml. xmlRoot = <multi_cactus inputSequences="1.fa 2.fa"> <tree>(Oar:1.0,Hu:1.0)Anc0;</tree> <cactus experiment_path="/tmp/tmpk9WIl_/progressiveAlignment/Anc0/Anc0_experiment.xml" name="Anc0" /> </multi_cactus> Importing 2 sequences Using the lsfbatch system Limiting maxCores to CPU count of system (28). Limiting maxMemory to physically available memory (270529912832). Created the workflow directory at /tmp/toil-7fd37406-ef95-403f-b4c1-4ae2ab6d0fe6-72618347f6d5763816d1354d0000004c Limiting maxDisk to physically available disk (176820895744). Batch system does not support hot-deployment. The user script ModuleDescriptor(dirPath='/home/cactus/lib/python2.7/site-packages', name='cactus.progressive.cactus_progressive', fromVirtualEnv=False) will have to be present at the same location on every worker. No user script to hot-deploy. Written the environment for the jobs to the environment file Caching all jobs in job store 0 jobs downloaded. Running Toil version 3.14.0-b91dbf9bf6116879952f0a70f9a2fbbcae7e51b6. Real-time logging disabled (Re)building internal scheduler state 2020-04-08 00:39:14,490 - toil.toilState - INFO - (Re)building internal scheduler state Found 1 jobs to start and 0 jobs with successors to run 2020-04-08 00:39:14,490 - toil.leader - INFO - Found 1 jobs to start and 0 jobs with successors to run Checked batch system has no running jobs and no updated jobs 2020-04-08 00:39:14,490 - toil.leader - INFO - Checked batch system has no running jobs and no updated jobs Starting the main loop 2020-04-08 00:39:14,491 - toil.leader - INFO - Starting the main loop bparams: invalid option -- 'a' Usage: bparams [-h] [-V] [-l] Invalid command <showconf> Usage: lsadmin [-h] [-V] [command] [command_options] [command_args] where 'command' is: reconfig Reconfigure jhscheduler ckconfig Check configuration files limrestart Restart LIM (Load Information Manager) limstartup Startup LIM (Load Information Manager) limshutdown Shut down LIM (Load Information Manager) limlock Lock LIM on local host limunlock Unlock LIM on local host resrestart Restart RES (Remote Execution Server) resstartup Startup RES (Remote Execution Server) resshutdown Shut down RES (Remote Execution Server) reslogon Log tasks executed by RES reslogoff RES log off limdebug Debug LIM limtime Debug LIM timing message resdebug Debug RES restime Debug RES timing message help Get help on commands ? Get help on commands quit Quit bparams: invalid option -- 'a' Usage: bparams [-h] [-V] [-l] Invalid command <showconf> Usage: lsadmin [-h] [-V] [command] [command_options] [command_args] ...... ......When I check my bparams, I got:
bparams -V JH UniScheduler 3.2, Feb 2 2016 Copyright (C) 2013 jhlava foundation. Copyright (C) 2011 openlava foundation. Copyright (C) 2007 Platform Computing Inc.I think the reason for this error may be that our bparams and other related software versions are too old, but I am not the root user and the server is difficult to upgrade in a short time, could you help me to solve it?
Thanks
-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/cactus/issues/205 Hi , I submit my jobs to LSF system with commad cactus --disableCaching --workDir /tmp --binariesMode local --batchSystem LSF jobStore cfg test.hal
But I got:
Root logger is at level 'INFO', 'toil' logger at level 'INFO'. Root logger is at level 'INFO', 'toil' logger at level 'INFO'. The workflow ID is: '7fd37406-ef95-403f-b4c1-4ae2ab6d0fe6' No branch length for test1: setting to 1 No branch length for test2: setting to 1 Using config from path /home/cactus/lib/python2.7/site-packages/cactus/cactus_progressive_config.xml. xmlRoot =
(Oar:1.0,Hu:1.0)Anc0; <cactus experiment_path="/tmp/tmpk9WIl_/progressiveAlignment/Anc0/Anc0_experiment.xml" name="Anc0" />Importing 2 sequences Using the lsfbatch system Limiting maxCores to CPU count of system (28). Limiting maxMemory to physically available memory (270529912832). Created the workflow directory at /tmp/toil-7fd37406-ef95-403f-b4c1-4ae2ab6d0fe6-72618347f6d5763816d1354d0000004c Limiting maxDisk to physically available disk (176820895744). Batch system does not support hot-deployment. The user script ModuleDescriptor(dirPath='/home/cactus/lib/python2.7/site-packages', name='cactus.progressive.cactus_progressive', fromVirtualEnv=False) will have to be present at the same location on every worker. No user script to hot-deploy. Written the environment for the jobs to the environment file Caching all jobs in job store 0 jobs downloaded. Running Toil version 3.14.0-b91dbf9bf6116879952f0a70f9a2fbbcae7e51b6. Real-time logging disabled (Re)building internal scheduler state 2020-04-08 00:39:14,490 - toil.toilState - INFO - (Re)building internal scheduler state Found 1 jobs to start and 0 jobs with successors to run 2020-04-08 00:39:14,490 - toil.leader - INFO - Found 1 jobs to start and 0 jobs with successors to run Checked batch system has no running jobs and no updated jobs 2020-04-08 00:39:14,490 - toil.leader - INFO - Checked batch system has no running jobs and no updated jobs Starting the main loop 2020-04-08 00:39:14,491 - toil.leader - INFO - Starting the main loop bparams: invalid option -- 'a' Usage: bparams [-h] [-V] [-l] Invalid command
Usage: lsadmin [-h] [-V] [command] [command_options] [command_args]
where 'command' is: reconfig Reconfigure jhscheduler ckconfig Check configuration files limrestart Restart LIM (Load Information Manager) limstartup Startup LIM (Load Information Manager) limshutdown Shut down LIM (Load Information Manager) limlock Lock LIM on local host limunlock Unlock LIM on local host resrestart Restart RES (Remote Execution Server) resstartup Startup RES (Remote Execution Server) resshutdown Shut down RES (Remote Execution Server) reslogon Log tasks executed by RES reslogoff RES log off limdebug Debug LIM limtime Debug LIM timing message resdebug Debug RES restime Debug RES timing message help Get help on commands ? Get help on commands quit Quitbparams: invalid option -- 'a' Usage: bparams [-h] [-V] [-l] Invalid command
Usage: lsadmin [-h] [-V] [command] [command_options] [command_args] ...... ......
When I check my bparams, I got:
bparams -V JH UniScheduler 3.2, Feb 2 2016 Copyright (C) 2013 jhlava foundation. Copyright (C) 2011 openlava foundation. Copyright (C) 2007 Platform Computing Inc.
I think the reason for this error may be that our bparams and other related software versions are too old, but I am not the root user and the server is difficult to upgrade in a short time, could you help me to solve it?
Thanks
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.*
Hi , I submitted my jobs to LSF system with commad
cactus --disableCaching --workDir /tmp --binariesMode local --batchSystem LSF jobStore cfg test.halBut I got:
When I checked my bparams, I got:
I think the reason for this error may be that our bparams and other related software versions are too old, but I am not the root user and the server is difficult to upgrade in a short time, could you help me to solve it?
Thanks