fix quotes, substitute container paths

virtualcell · Sep 27, 2024 · 2929f8c · 2929f8c
1 parent 8ebbdba
commit 2929f8c
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Showing 12 changed files with 104 additions and 67 deletions.
diff --git a/vcell-server/src/main/java/cbit/vcell/message/server/htc/slurm/SlurmProxy.java b/vcell-server/src/main/java/cbit/vcell/message/server/htc/slurm/SlurmProxy.java
@@ -46,6 +46,12 @@ public String getPrefix() {
 			return prefix;
 		}
 	}
+
+	private record SingularityBinding(String hostPath, String containerPath) {
+		public String getBinding() {
+			return "--bind "+hostPath+":"+containerPath;
+		}
+	}
 
 	public SlurmProxy(CommandService commandService, String htcUser) {
 		super(commandService, htcUser);
@@ -478,17 +484,28 @@ SbatchSolverComponents generateScript(String jobName, ExecutableCommand.Containe
 				"serverid="+serverid
 		};
 
+		List<SingularityBinding> bindings = List.of(
+				new SingularityBinding(primaryDataDirExternal, "/simdata"),
+				new SingularityBinding(secondaryDataDirExternal, "/simdata_secondary"),
+				new SingularityBinding(simDataDirArchiveExternal, simDataDirArchiveInternal),
+				new SingularityBinding(htclogdir_external, "/htclogs"),
+				new SingularityBinding(slurm_tmpdir, "/solvertmp")
+		);
+
 		LineStringBuilder lsb = new LineStringBuilder();
 		LineStringBuilder singularityLSB = new LineStringBuilder();
-		slurmInitSingularity(singularityLSB, primaryDataDirExternal, Optional.of(secondaryDataDirExternal), htclogdir_external,
-				solverDockerName, Optional.of(batchDockerName),
+		slurmInitSingularity(singularityLSB,
+				solverDockerName, Optional.of(batchDockerName), bindings,
 				slurm_tmpdir, slurm_singularity_cachedir, slurm_singularity_pullfolder,
-				simDataDirArchiveExternal, simDataDirArchiveInternal,
 				slurm_singularity_module_name, environmentVars);
 
 		LineStringBuilder sendFailMsgLSB = new LineStringBuilder();
 		sendFailMsgScript(simTask, sendFailMsgLSB, jmshost_sim_external, jmsport_sim_external, jmsuser, jmspswd);
-
+
+		for (SingularityBinding binding : bindings) {
+			commandSet.translatePaths(new File(binding.hostPath), new File(binding.containerPath));
+		}
+
 		final boolean hasExitProcessor = commandSet.hasExitCodeCommand();
 	//	lsb.write("run_in_container=\"singularity /path/to/data:/simdata /path/to/image/vcell-batch.img);
 		LineStringBuilder callExitLSB = new LineStringBuilder();
@@ -498,6 +515,7 @@ SbatchSolverComponents generateScript(String jobName, ExecutableCommand.Containe
 
 		LineStringBuilder preProcessLSB = new LineStringBuilder();
 		for (ExecutableCommand ec: commandSet.getExecCommands()) {
+			ExecutableCommand.Container commandSet2 = new ExecutableCommand.Container();
 			if(ec.getCommands().get(0).equals("JavaPreprocessor64")) {
 				execCommandScript(preProcessLSB, hasExitProcessor, ec, "${batch_container_prefix}");
 			}else {
@@ -526,7 +544,7 @@ private void callExitScript(ExecutableCommand.Container commandSet, LineStringBu
 		exitCmd.stripPathFromCommand();
 		lsb.write("callExitProcessor( ) {");
 		lsb.append('\t');
-		lsb.write("\"${batch_container_prefix} " + exitCmd.getJoinedCommands("$1")+"\"");
+		lsb.write("${batch_container_prefix} " + exitCmd.getJoinedCommands("$1").trim());
 		lsb.write("}");
 		lsb.newline();
 		lsb.newline();
@@ -563,7 +581,7 @@ private void sendFailMsgScript(SimulationTask simTask, LineStringBuilder lsb, St
 	private void execCommandScript(LineStringBuilder lsb,final boolean hasExitProcessor, ExecutableCommand ec, String container_prefix) {
 		ec.stripPathFromCommand();
 		String cmd= ec.getJoinedCommands();
-		lsb.write("\"" + container_prefix + " " + cmd + "\"");
+		lsb.write(container_prefix + " " + cmd.trim());
 		lsb.write("stat=$?");
 		lsb.append("echo returned $stat");
 		lsb.newline();
@@ -578,11 +596,10 @@ private void execCommandScript(LineStringBuilder lsb,final boolean hasExitProces
 	}
 
 
-	private void slurmInitSingularity(LineStringBuilder lsb, String primaryDataDirExternal,
-				  Optional<String> secondaryDataDirExternal, String htclogdir_external,
-				  String solverDockerName, Optional<String> batchDockerName,
+	private void slurmInitSingularity(LineStringBuilder lsb,
+				  String solverDockerName, Optional<String> batchDockerName, List<SingularityBinding> bindings,
 				  String slurm_tmpdir, String slurm_singularity_cachedir, String slurm_singularity_pullfolder,
-				  String simDataDirArchiveExternal, String simDataDirArchiveInternal, String singularity_module_name, String[] environmentVars) {
+				  String singularity_module_name, String[] environmentVars) {
 		lsb.write("TMPDIR="+slurm_tmpdir);
 		lsb.write("if [ ! -e $TMPDIR ]; then mkdir -p $TMPDIR ; fi");
 
@@ -603,11 +620,14 @@ private void slurmInitSingularity(LineStringBuilder lsb, String primaryDataDirEx
 		lsb.write("env");
 		lsb.newline();
 
-		lsb.write("container_bindings=\"--bind "+primaryDataDirExternal+":/simdata \"");
-		lsb.write("container_bindings+=\"--bind "+slurm_tmpdir+":/solvertmp \"");
-		lsb.write("container_bindings+=\"--bind "+htclogdir_external+":/htclogs \"");
-		if (secondaryDataDirExternal.isPresent()) {
-			lsb.write("container_bindings+=\"--bind "+secondaryDataDirExternal.get()+":/simdata_secondary \"");
+		boolean bFirstBind=true;
+		for (SingularityBinding binding : bindings) {
+			if (bFirstBind) {
+				lsb.write("container_bindings=\"--bind " + binding.hostPath + ":" + binding.containerPath + " \"");
+				bFirstBind = false;
+			}else{
+				lsb.write("container_bindings+=\"--bind " + binding.hostPath + ":" + binding.containerPath + " \"");
+			}
 		}
 		boolean bFirstEnv=true;
 		for (String envVar : environmentVars) {
@@ -761,10 +781,16 @@ String createOptJobScript(String jobName, File optProblemInputFile, File optProb
 		if (!optDataDirExternal.exists() && !optDataDirExternal.mkdir()){
 			LG.error("failed to make optimization data directory "+optDataDir.getAbsolutePath());
 		}
-//			if (optDataDirExternal.setWritable(true,false))
-		slurmInitSingularity(lsb, optDataDirExternal.getAbsolutePath(), Optional.empty(), htclogdir_external, solverDockerName, batchDockerName,
-				slurm_tmpdir, slurm_singularity_cachedir, slurm_singularity_pullfolder,
-				simDataDirArchiveExternal, simDataDirArchiveInternal,
+
+		List<SingularityBinding> bindings = List.of(
+				new SingularityBinding(optDataDirExternal.getAbsolutePath(), "/simdata"),
+				new SingularityBinding(slurm_tmpdir, "/solvertmp"),
+				new SingularityBinding(htclogdir_external, "/htclogs"),
+				new SingularityBinding(simDataDirArchiveExternal, simDataDirArchiveInternal)
+		);
+
+		slurmInitSingularity(lsb, solverDockerName, batchDockerName,
+				bindings, slurm_tmpdir, slurm_singularity_cachedir, slurm_singularity_pullfolder,
 				slurm_singularity_module_name, environmentVars);
 
 		lsb.write("cmd_prefix=\"$solver_container_prefix\"");

diff --git a/vcell-server/src/test/resources/slurm_fixtures/adams_moulton/V_REL_274633859_0_0.slurm.sub b/vcell-server/src/test/resources/slurm_fixtures/adams_moulton/V_REL_274633859_0_0.slurm.sub
@@ -25,9 +25,10 @@ echo ENVIRONMENT
 env
 
 container_bindings="--bind /share/apps/vcell3/users:/simdata "
-container_bindings+="--bind /scratch/vcell:/solvertmp "
-container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
 container_bindings+="--bind /share/apps/vcell7/users:/simdata_secondary "
+container_bindings+="--bind /share/apps/vcell12/users:/share/apps/vcell12/users "
+container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
+container_bindings+="--bind /scratch/vcell:/solvertmp "
 container_env="--env java_mem_Xmx=4096M "
 container_env+="--env jmshost_sim_internal=rke-wn-01.cam.uchc.edu "
 container_env+="--env jmsport_sim_internal=31618 "
@@ -61,11 +62,11 @@ sendFailureMsg() {
 
 
 callExitProcessor( ) {
-	"${batch_container_prefix} JavaPostprocessor64 274633859 schaff 17 0 0 $1 /share/apps/vcell3/htclogs/V_REL_274633859_0_0.slurm.sub "
+	${batch_container_prefix} JavaPostprocessor64 274633859 schaff 17 0 0 $1 /htclogs/V_REL_274633859_0_0.slurm.sub
 }
 
 
-"${solver_container_prefix} JavaSimExe64 /share/apps/vcell3/users/schaff/SimID_274633859_0__0.simtask.xml /share/apps/vcell3/users/schaff "
+${solver_container_prefix} JavaSimExe64 /simdata/schaff/SimID_274633859_0__0.simtask.xml /simdata/schaff
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then

diff --git a/vcell-server/src/test/resources/slurm_fixtures/cvode/V_REL_274630682_0_0.slurm.sub b/vcell-server/src/test/resources/slurm_fixtures/cvode/V_REL_274630682_0_0.slurm.sub
@@ -25,9 +25,10 @@ echo ENVIRONMENT
 env
 
 container_bindings="--bind /share/apps/vcell3/users:/simdata "
-container_bindings+="--bind /scratch/vcell:/solvertmp "
-container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
 container_bindings+="--bind /share/apps/vcell7/users:/simdata_secondary "
+container_bindings+="--bind /share/apps/vcell12/users:/share/apps/vcell12/users "
+container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
+container_bindings+="--bind /scratch/vcell:/solvertmp "
 container_env="--env java_mem_Xmx=4096M "
 container_env+="--env jmshost_sim_internal=rke-wn-01.cam.uchc.edu "
 container_env+="--env jmsport_sim_internal=31618 "
@@ -61,11 +62,11 @@ sendFailureMsg() {
 
 
 callExitProcessor( ) {
-	"${batch_container_prefix} JavaPostprocessor64 274630682 schaff 17 0 0 $1 /share/apps/vcell3/htclogs/V_REL_274630682_0_0.slurm.sub "
+	${batch_container_prefix} JavaPostprocessor64 274630682 schaff 17 0 0 $1 /htclogs/V_REL_274630682_0_0.slurm.sub
 }
 
 
-"${batch_container_prefix} JavaPreprocessor64 /share/apps/vcell3/users/schaff/SimID_274630682_0__0.simtask.xml /share/apps/vcell3/users/schaff "
+${batch_container_prefix} JavaPreprocessor64 /simdata/schaff/SimID_274630682_0__0.simtask.xml /simdata/schaff
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then
@@ -74,7 +75,7 @@ if [ $stat -ne 0 ]; then
 	exit $stat
 fi
 
-"${solver_container_prefix} SundialsSolverStandalone_x64 /share/apps/vcell3/users/schaff/SimID_274630682_0_.cvodeInput /share/apps/vcell3/users/schaff/SimID_274630682_0_.ida -tid 0 "
+${solver_container_prefix} SundialsSolverStandalone_x64 /simdata/schaff/SimID_274630682_0_.cvodeInput /simdata/schaff/SimID_274630682_0_.ida -tid 0
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then

diff --git a/vcell-server/src/test/resources/slurm_fixtures/finite_volume/V_REL_274514696_0_0.slurm.sub b/vcell-server/src/test/resources/slurm_fixtures/finite_volume/V_REL_274514696_0_0.slurm.sub
@@ -25,9 +25,10 @@ echo ENVIRONMENT
 env
 
 container_bindings="--bind /share/apps/vcell3/users:/simdata "
-container_bindings+="--bind /scratch/vcell:/solvertmp "
-container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
 container_bindings+="--bind /share/apps/vcell7/users:/simdata_secondary "
+container_bindings+="--bind /share/apps/vcell12/users:/share/apps/vcell12/users "
+container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
+container_bindings+="--bind /scratch/vcell:/solvertmp "
 container_env="--env java_mem_Xmx=4096M "
 container_env+="--env jmshost_sim_internal=rke-wn-01.cam.uchc.edu "
 container_env+="--env jmsport_sim_internal=31618 "
@@ -61,11 +62,11 @@ sendFailureMsg() {
 
 
 callExitProcessor( ) {
-	"${batch_container_prefix} JavaPostprocessor64 274514696 schaff 17 0 0 $1 /share/apps/vcell3/htclogs/V_REL_274514696_0_0.slurm.sub "
+	${batch_container_prefix} JavaPostprocessor64 274514696 schaff 17 0 0 $1 /htclogs/V_REL_274514696_0_0.slurm.sub
 }
 
 
-"${batch_container_prefix} JavaPreprocessor64 /share/apps/vcell3/users/schaff/SimID_274514696_0__0.simtask.xml /share/apps/vcell3/users/schaff "
+${batch_container_prefix} JavaPreprocessor64 /simdata/schaff/SimID_274514696_0__0.simtask.xml /simdata/schaff
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then
@@ -74,7 +75,7 @@ if [ $stat -ne 0 ]; then
 	exit $stat
 fi
 
-"${solver_container_prefix} FiniteVolume_x64 /share/apps/vcell3/users/schaff/SimID_274514696_0_.fvinput -tid 0 "
+${solver_container_prefix} FiniteVolume_x64 /simdata/schaff/SimID_274514696_0_.fvinput -tid 0
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then

diff --git a/vcell-server/src/test/resources/slurm_fixtures/gibson/V_REL_274635122_0_0.slurm.sub b/vcell-server/src/test/resources/slurm_fixtures/gibson/V_REL_274635122_0_0.slurm.sub
@@ -25,9 +25,10 @@ echo ENVIRONMENT
 env
 
 container_bindings="--bind /share/apps/vcell3/users:/simdata "
-container_bindings+="--bind /scratch/vcell:/solvertmp "
-container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
 container_bindings+="--bind /share/apps/vcell7/users:/simdata_secondary "
+container_bindings+="--bind /share/apps/vcell12/users:/share/apps/vcell12/users "
+container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
+container_bindings+="--bind /scratch/vcell:/solvertmp "
 container_env="--env java_mem_Xmx=4096M "
 container_env+="--env jmshost_sim_internal=rke-wn-01.cam.uchc.edu "
 container_env+="--env jmsport_sim_internal=31618 "
@@ -61,11 +62,11 @@ sendFailureMsg() {
 
 
 callExitProcessor( ) {
-	"${batch_container_prefix} JavaPostprocessor64 274635122 schaff 17 0 0 $1 /share/apps/vcell3/htclogs/V_REL_274635122_0_0.slurm.sub "
+	${batch_container_prefix} JavaPostprocessor64 274635122 schaff 17 0 0 $1 /htclogs/V_REL_274635122_0_0.slurm.sub
 }
 
 
-"${batch_container_prefix} JavaPreprocessor64 /share/apps/vcell3/users/schaff/SimID_274635122_0__0.simtask.xml /share/apps/vcell3/users/schaff "
+${batch_container_prefix} JavaPreprocessor64 /simdata/schaff/SimID_274635122_0__0.simtask.xml /simdata/schaff
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then
@@ -74,7 +75,7 @@ if [ $stat -ne 0 ]; then
 	exit $stat
 fi
 
-"${solver_container_prefix} VCellStoch_x64 gibson /share/apps/vcell3/users/schaff/SimID_274635122_0_.stochInput /share/apps/vcell3/users/schaff/SimID_274635122_0_.ida -tid 0 "
+${solver_container_prefix} VCellStoch_x64 gibson /simdata/schaff/SimID_274635122_0_.stochInput /simdata/schaff/SimID_274635122_0_.ida -tid 0
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then

diff --git a/vcell-server/src/test/resources/slurm_fixtures/gibson_milstein/V_REL_274641698_0_0.slurm.sub b/vcell-server/src/test/resources/slurm_fixtures/gibson_milstein/V_REL_274641698_0_0.slurm.sub
@@ -25,9 +25,10 @@ echo ENVIRONMENT
 env
 
 container_bindings="--bind /share/apps/vcell3/users:/simdata "
-container_bindings+="--bind /scratch/vcell:/solvertmp "
-container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
 container_bindings+="--bind /share/apps/vcell7/users:/simdata_secondary "
+container_bindings+="--bind /share/apps/vcell12/users:/share/apps/vcell12/users "
+container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
+container_bindings+="--bind /scratch/vcell:/solvertmp "
 container_env="--env java_mem_Xmx=4096M "
 container_env+="--env jmshost_sim_internal=rke-wn-01.cam.uchc.edu "
 container_env+="--env jmsport_sim_internal=31618 "
@@ -61,11 +62,11 @@ sendFailureMsg() {
 
 
 callExitProcessor( ) {
-	"${batch_container_prefix} JavaPostprocessor64 274641698 schaff 17 0 0 $1 /share/apps/vcell3/htclogs/V_REL_274641698_0_0.slurm.sub "
+	${batch_container_prefix} JavaPostprocessor64 274641698 schaff 17 0 0 $1 /htclogs/V_REL_274641698_0_0.slurm.sub
 }
 
 
-"${batch_container_prefix} JavaPreprocessor64 /share/apps/vcell3/users/schaff/SimID_274641698_0__0.simtask.xml /share/apps/vcell3/users/schaff "
+${batch_container_prefix} JavaPreprocessor64 /simdata/schaff/SimID_274641698_0__0.simtask.xml /simdata/schaff
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then
@@ -74,7 +75,7 @@ if [ $stat -ne 0 ]; then
 	exit $stat
 fi
 
-"${solver_container_prefix} Hybrid_EM_x64 /share/apps/vcell3/users/schaff/SimID_274641698_0_.nc 100.0 10.0 0.01 0.1 -OV -tid 0 "
+${solver_container_prefix} Hybrid_EM_x64 /simdata/schaff/SimID_274641698_0_.nc 100.0 10.0 0.01 0.1 -OV -tid 0
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then

diff --git a/vcell-server/src/test/resources/slurm_fixtures/langevin/V_REL_274672135_0_0.slurm.sub b/vcell-server/src/test/resources/slurm_fixtures/langevin/V_REL_274672135_0_0.slurm.sub
@@ -25,9 +25,10 @@ echo ENVIRONMENT
 env
 
 container_bindings="--bind /share/apps/vcell3/users:/simdata "
-container_bindings+="--bind /scratch/vcell:/solvertmp "
-container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
 container_bindings+="--bind /share/apps/vcell7/users:/simdata_secondary "
+container_bindings+="--bind /share/apps/vcell12/users:/share/apps/vcell12/users "
+container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
+container_bindings+="--bind /scratch/vcell:/solvertmp "
 container_env="--env java_mem_Xmx=4096M "
 container_env+="--env jmshost_sim_internal=rke-wn-01.cam.uchc.edu "
 container_env+="--env jmsport_sim_internal=31618 "
@@ -61,11 +62,11 @@ sendFailureMsg() {
 
 
 callExitProcessor( ) {
-	"${batch_container_prefix} JavaPostprocessor64 274672135 schaff 17 0 0 $1 /share/apps/vcell3/htclogs/V_REL_274672135_0_0.slurm.sub "
+	${batch_container_prefix} JavaPostprocessor64 274672135 schaff 17 0 0 $1 /htclogs/V_REL_274672135_0_0.slurm.sub
 }
 
 
-"${batch_container_prefix} JavaPreprocessor64 /share/apps/vcell3/users/schaff/SimID_274672135_0__0.simtask.xml /share/apps/vcell3/users/schaff "
+${batch_container_prefix} JavaPreprocessor64 /simdata/schaff/SimID_274672135_0__0.simtask.xml /simdata/schaff
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then
@@ -74,7 +75,7 @@ if [ $stat -ne 0 ]; then
 	exit $stat
 fi
 
-"${solver_container_prefix} langevin_x64 simulate --output-log=/share/apps/vcell3/users/schaff/SimID_274672135_0_.log --vc-send-status-config=/share/apps/vcell3/users/schaff/SimID_274672135_0_.langevinMessagingConfig /share/apps/vcell3/users/schaff/SimID_274672135_0_.langevinInput 0 -tid 0 "
+${solver_container_prefix} langevin_x64 simulate --output-log=/simdata/schaff/SimID_274672135_0_.log --vc-send-status-config=/simdata/schaff/SimID_274672135_0_.langevinMessagingConfig /simdata/schaff/SimID_274672135_0_.langevinInput 0 -tid 0
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then

diff --git a/vcell-server/src/test/resources/slurm_fixtures/moving_boundary/V_REL_274641196_0_0.slurm.sub b/vcell-server/src/test/resources/slurm_fixtures/moving_boundary/V_REL_274641196_0_0.slurm.sub
@@ -25,9 +25,10 @@ echo ENVIRONMENT
 env
 
 container_bindings="--bind /share/apps/vcell3/users:/simdata "
-container_bindings+="--bind /scratch/vcell:/solvertmp "
-container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
 container_bindings+="--bind /share/apps/vcell7/users:/simdata_secondary "
+container_bindings+="--bind /share/apps/vcell12/users:/share/apps/vcell12/users "
+container_bindings+="--bind /share/apps/vcell3/htclogs:/htclogs "
+container_bindings+="--bind /scratch/vcell:/solvertmp "
 container_env="--env java_mem_Xmx=4096M "
 container_env+="--env jmshost_sim_internal=rke-wn-01.cam.uchc.edu "
 container_env+="--env jmsport_sim_internal=31618 "
@@ -61,11 +62,11 @@ sendFailureMsg() {
 
 
 callExitProcessor( ) {
-	"${batch_container_prefix} JavaPostprocessor64 274641196 schaff 17 0 0 $1 /share/apps/vcell3/htclogs/V_REL_274641196_0_0.slurm.sub "
+	${batch_container_prefix} JavaPostprocessor64 274641196 schaff 17 0 0 $1 /htclogs/V_REL_274641196_0_0.slurm.sub
 }
 
 
-"${batch_container_prefix} JavaPreprocessor64 /share/apps/vcell3/users/schaff/SimID_274641196_0__0.simtask.xml /share/apps/vcell3/users/schaff "
+${batch_container_prefix} JavaPreprocessor64 /simdata/schaff/SimID_274641196_0__0.simtask.xml /simdata/schaff
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then
@@ -74,7 +75,7 @@ if [ $stat -ne 0 ]; then
 	exit $stat
 fi
 
-"${solver_container_prefix} MovingBoundary_x64 --config /share/apps/vcell3/users/schaff/SimID_274641196_0_mb.xml -tid 0 "
+${solver_container_prefix} MovingBoundary_x64 --config /simdata/schaff/SimID_274641196_0_mb.xml -tid 0
 stat=$?
 echo returned $stat
 if [ $stat -ne 0 ]; then