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add --containall singularity flag to better isolate containers from host
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@jcschaff @AvocadoMoon
jcschaff authored and AvocadoMoon committed Sep 20, 2024
1 parent a231a5d commit 8897d50
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Showing 12 changed files with 12 additions and 12 deletions.
2 changes: 1 addition & 1 deletion vcell-server/src/main/java/cbit/vcell/message/server/htc/slurm/SlurmProxy.java
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Expand Up @@ -753,7 +753,7 @@ private void slurmInitSingularity(LineStringBuilder lsb, String primaryDataDirEx
for (String envVar : environmentVars) {
singularityEnvironmentVars.append(" --env "+envVar);
}
lsb.write(" container_prefix=\"singularity run " +
lsb.write(" container_prefix=\"singularity run --containall " +
"--bind "+primaryDataDirExternal+":/simdata " +
((secondaryDataDirExternal.isPresent()) ? "--bind "+secondaryDataDirExternal.get()+":/simdata_secondary " : "") +
"--bind "+simDataDirArchiveExternal+":"+simDataDirArchiveInternal+" " +
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/adams_moulton/V_REL_274633859_0_0.slurm.sub
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Expand Up @@ -77,7 +77,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/cvode/V_REL_274630682_0_0.slurm.sub
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Expand Up @@ -77,7 +77,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/finite_volume/V_REL_274514696_0_0.slurm.sub
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Expand Up @@ -77,7 +77,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/gibson/V_REL_274635122_0_0.slurm.sub
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Expand Up @@ -77,7 +77,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/gibson_milstein/V_REL_274641698_0_0.slurm.sub
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Expand Up @@ -77,7 +77,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/langevin/V_REL_274672135_0_0.slurm.sub
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Expand Up @@ -77,7 +77,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/moving_boundary/V_REL_274641196_0_0.slurm.sub
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Expand Up @@ -77,7 +77,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/nfsim/V_REL_274642453_0_0.slurm.sub
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Expand Up @@ -77,7 +77,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-batch_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users:/simdata --bind /share/apps/vcell7/users:/simdata_secondary --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env java_mem_Xmx=4096M --env jmshost_sim_internal=rke-wn-01.cam.uchc.edu --env jmsport_sim_internal=31618 --env jmsrestport_sim_internal=30163 --env jmsuser=clientUser --env jmspswd=dummy --env jmsblob_minsize=100000 --env mongodbhost_internal=rke-wn-01.cam.uchc.edu --env mongodbport_internal=30019 --env mongodb_database=test --env primary_datadir_external=/share/apps/vcell3/users --env secondary_datadir_external=/share/apps/vcell7/users --env htclogdir_external=/share/apps/vcell3/htclogs --env softwareVersion=Rel_Version_7.6.0_build_28 --env serverid=REL "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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2 changes: 1 addition & 1 deletion vcell-server/src/test/resources/slurm_fixtures/opt/CopasiParest_152878.sub
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Expand Up @@ -75,7 +75,7 @@ if command -v singularity >/dev/null 2>&1; then
echo successful copy from /share/apps/vcell3/singularityImages/ghcr.io_virtualcell_vcell-opt_d6825f4.img to /state/partition1/singularityImages/ghcr.io_virtualcell_vcell-opt_d6825f4.img
fi
fi
container_prefix="singularity run --bind /share/apps/vcell3/users/parest_data:/simdata --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env datadir_external=/share/apps/vcell3/users "
container_prefix="singularity run --containall --bind /share/apps/vcell3/users/parest_data:/simdata --bind /share/apps/vcell12/users:/share/apps/vcell12/users --bind /share/apps/vcell3/htclogs:/htclogs --bind /scratch/vcell:/solvertmp $localSingularityImage --env datadir_external=/share/apps/vcell3/users "
else
echo "Required singularity command not found (maybe 'module load singularity/vcell-3.10.0' command didn't work) "
exit 1
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