From d2c9a43641f01f9f9a2917a529eabb19dec9ef4a Mon Sep 17 00:00:00 2001 From: Adrian Fraiha Date: Fri, 1 May 2020 12:26:38 -0400 Subject: [PATCH 1/3] initial --- submitter/jobsubmitter.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/submitter/jobsubmitter.py b/submitter/jobsubmitter.py index 8d3cfbd9..96e8608f 100644 --- a/submitter/jobsubmitter.py +++ b/submitter/jobsubmitter.py @@ -104,6 +104,16 @@ def _prepare_directories(self): os.mkdir(self.job_tmp_dir) def _command_line(self): + """ + Start ACCESS-specific code + In addition to different arguments and required bins, ACCESS requires a specific version of Toil that prevents the following PATH from recursively appending itself on every job, causing "OSExit Too many argument". + """ + path = "PATH=/work/access/testing/users/fraihaa/ridgeback/conda/envs/toil-msk-3.21.1-MSK-rc1/bin:/conda/bin:/home/accessbot/miniconda3/envs/ACCESS_1.3.26/bin/:{}".format(os.environ.get('PATH')) + command_line = [path, 'toil-cwl-runner', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--logLevel', 'DEBUG','--disable-host-provenance','--stats', '--debug', '--cleanWorkDir', 'always', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '_JAVA_OPTIONS', 'PYTHONPATH', 'TEMP', '--defaultMemory', '10G', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir] + """ + End ACCESS-specific code + """ + command_line = [settings.CWLTOIL, '--singularity', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--disable-host-provenance','--stats', '--debug', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '--defaultMemory', '8G', '--maxCores', '16', '--maxDisk', '128G', '--maxMemory', '256G', '--not-strict', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir, '--maxLocalJobs', '500'] app_location, inputs_location = self._dump_app_inputs() if self.resume_jobstore: From 13f7279ba34513a9869fbced35719265246bfb6b Mon Sep 17 00:00:00 2001 From: Adrian Fraiha Date: Wed, 13 May 2020 09:26:55 -0400 Subject: [PATCH 2/3] update paths for now --- submitter/jobsubmitter.py | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/submitter/jobsubmitter.py b/submitter/jobsubmitter.py index 96e8608f..987c95fd 100644 --- a/submitter/jobsubmitter.py +++ b/submitter/jobsubmitter.py @@ -104,17 +104,21 @@ def _prepare_directories(self): os.mkdir(self.job_tmp_dir) def _command_line(self): - """ - Start ACCESS-specific code - In addition to different arguments and required bins, ACCESS requires a specific version of Toil that prevents the following PATH from recursively appending itself on every job, causing "OSExit Too many argument". - """ - path = "PATH=/work/access/testing/users/fraihaa/ridgeback/conda/envs/toil-msk-3.21.1-MSK-rc1/bin:/conda/bin:/home/accessbot/miniconda3/envs/ACCESS_1.3.26/bin/:{}".format(os.environ.get('PATH')) - command_line = [path, 'toil-cwl-runner', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--logLevel', 'DEBUG','--disable-host-provenance','--stats', '--debug', '--cleanWorkDir', 'always', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '_JAVA_OPTIONS', 'PYTHONPATH', 'TEMP', '--defaultMemory', '10G', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir] - """ - End ACCESS-specific code - """ - - command_line = [settings.CWLTOIL, '--singularity', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--disable-host-provenance','--stats', '--debug', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '--defaultMemory', '8G', '--maxCores', '16', '--maxDisk', '128G', '--maxMemory', '256G', '--not-strict', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir, '--maxLocalJobs', '500'] + + if "access" in self.app.github.lower(): + """ + Start ACCESS-specific code + In addition to different arguments and required bins, ACCESS requires a specific version of Toil that prevents the following PATH from recursively appending itself on every job, causing "OSExit Too many argument". + """ + path = "PATH=:/juno/work/ci/access-pipelines/miniconda3/envs/ACCESS_1.3.26/bin:/juno/work/ci/access-pipelines/toil-msk-3.21.1-MSK-rc1/bin:{}".format(os.environ.get('PATH')) + command_line = [path, 'toil-cwl-runner', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--logLevel', 'DEBUG','--disable-host-provenance','--stats', '--debug', '--cleanWorkDir', 'always', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '_JAVA_OPTIONS', 'PYTHONPATH', 'TEMP', '--defaultMemory', '10G', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir] + """ + End ACCESS-specific code + """ + else: + command_line = [settings.CWLTOIL, '--singularity', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--disable-host-provenance','--stats', '--debug', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '--defaultMemory', '8G', '--maxCores', '16', '--maxDisk', '128G', '--maxMemory', '256G', '--not-strict', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir, '--maxLocalJobs', '500'] + + app_location, inputs_location = self._dump_app_inputs() if self.resume_jobstore: command_line.extend(['--restart',app_location]) From 6652710dbb18e82ae80c941181780e4009ea2948 Mon Sep 17 00:00:00 2001 From: Adrian Fraiha Date: Fri, 15 May 2020 12:38:19 -0400 Subject: [PATCH 3/3] Update jobsubmitter.py --- submitter/jobsubmitter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/submitter/jobsubmitter.py b/submitter/jobsubmitter.py index 987c95fd..bf73987a 100644 --- a/submitter/jobsubmitter.py +++ b/submitter/jobsubmitter.py @@ -110,7 +110,7 @@ def _command_line(self): Start ACCESS-specific code In addition to different arguments and required bins, ACCESS requires a specific version of Toil that prevents the following PATH from recursively appending itself on every job, causing "OSExit Too many argument". """ - path = "PATH=:/juno/work/ci/access-pipelines/miniconda3/envs/ACCESS_1.3.26/bin:/juno/work/ci/access-pipelines/toil-msk-3.21.1-MSK-rc1/bin:{}".format(os.environ.get('PATH')) + path = "PATH=/juno/work/ci/access-pipelines/toil-msk-3.21.1-MSK-rc1/bin:/juno/work/ci/access-pipelines/miniconda3/envs/ACCESS_1.3.26/bin:{}".format(os.environ.get('PATH')) command_line = [path, 'toil-cwl-runner', '--logFile', 'toil_log.log', '--batchSystem','lsf','--disable-user-provenance','--logLevel', 'DEBUG','--disable-host-provenance','--stats', '--debug', '--cleanWorkDir', 'always', '--disableCaching', '--preserve-environment', 'PATH', 'TMPDIR', 'TOIL_LSF_ARGS', 'SINGULARITY_PULLDIR', 'SINGULARITY_CACHEDIR', 'PWD', '_JAVA_OPTIONS', 'PYTHONPATH', 'TEMP', '--defaultMemory', '10G', '--realTimeLogging', '--jobStore', self.job_store_dir, '--tmpdir-prefix', self.job_tmp_dir, '--workDir', self.job_work_dir, '--outdir', self.job_outputs_dir] """ End ACCESS-specific code