Merge pull request #5 from mathworks/v2.2.1

v2.2.1

Author: jmcave

README.md

@@ -139,7 +139,7 @@ By modifying the plugins, you can add support for your own custom `AdditionalPro
 To manage work on the cluster, MATLAB calls the Grid Engine command line utilities.
 For example, the `qsub` command to submit work and `qstat` to query the state of submitted jobs.
 If your MATLAB session is running on a machine with the scheduler utilities available, the plugin scripts can call the utilities on the command line.
-Scheduler utilties are typically available if your MATLAB session is running on the Grid Engine cluster to which you want to submit.
+Scheduler utilities are typically available if your MATLAB session is running on the Grid Engine cluster to which you want to submit.
 
 If MATLAB cannot directly access the scheduler utilities on the command line, the plugin scripts create an SSH session to the cluster and run scheduler commands over that connection.
 To configure your cluster to submit scheduler commands via SSH, set the `ClusterHost` field of `AdditionalProperties` to the name of the cluster node to which MATLAB connects via SSH.

communicatingJobWrapper.sh

@@ -18,7 +18,7 @@
 # The following environment variables are set by Grid Engine:
 # PE_HOSTFILE - list of hostnames with their associated number of processors allocated to this Grid Engine job
 
-# Copyright 2006-2023 The MathWorks, Inc.
+# Copyright 2006-2024 The MathWorks, Inc.
 
 # If PARALLEL_SERVER_ environment variables are not set, assign any
 # available values with form MDCE_ for backwards compatibility
@@ -28,6 +28,9 @@ PARALLEL_SERVER_MATLAB_ARGS=${PARALLEL_SERVER_MATLAB_ARGS:="${MDCE_MATLAB_ARGS}"
 PARALLEL_SERVER_NUM_THREADS=${PARALLEL_SERVER_NUM_THREADS:="${MDCE_NUM_THREADS}"}
 PARALLEL_SERVER_DEBUG=${PARALLEL_SERVER_DEBUG:="${MDCE_DEBUG}"}
 
+# Other environment variables to forward
+PARALLEL_SERVER_GENVLIST="${PARALLEL_SERVER_GENVLIST},HOME,USER"
+
 # Echo the resources that the scheduler has allocated to this job:
 echo -e "The scheduler has allocated the following resources to this job (format is [hostname] [number of parallel processes to run on host] [queue name] [processor range]):\n$(cat ${PE_HOSTFILE:?"Host file undefined"})"
 
@@ -42,12 +45,13 @@ if [ ! -z "${PARALLEL_SERVER_DEBUG}" ] && [ "${PARALLEL_SERVER_DEBUG}" != "false
     MPI_VERBOSE="${MPI_VERBOSE} -v -print-all-exitcodes"
 fi
 
-# Unset the hostname variables to ensure they don't get forwarded by mpiexec
-unset HOST HOSTNAME
-
 # Construct the command to run.
-CMD="\"${FULL_MPIEXEC}\" -bind-to core:${PARALLEL_SERVER_NUM_THREADS} ${MPI_VERBOSE} \
-    \"${PARALLEL_SERVER_MATLAB_EXE}\" ${PARALLEL_SERVER_MATLAB_ARGS}"
+CMD="\"${FULL_MPIEXEC}\" \
+    -genvlist ${PARALLEL_SERVER_GENVLIST} \
+    -bind-to core:${PARALLEL_SERVER_NUM_THREADS} \
+    ${MPI_VERBOSE} \
+    \"${PARALLEL_SERVER_MATLAB_EXE}\" \
+    ${PARALLEL_SERVER_MATLAB_ARGS}"
 
 # Echo the command so that it is shown in the output log.
 echo $CMD

communicatingJobWrapperSmpd.sh

@@ -24,6 +24,9 @@ PARALLEL_SERVER_CMR=${PARALLEL_SERVER_CMR:="${MDCE_CMR}"}
 PARALLEL_SERVER_MATLAB_EXE=${PARALLEL_SERVER_MATLAB_EXE:="${MDCE_MATLAB_EXE}"}
 PARALLEL_SERVER_MATLAB_ARGS=${PARALLEL_SERVER_MATLAB_ARGS:="${MDCE_MATLAB_ARGS}"}
 
+# Other environment variables to forward
+PARALLEL_SERVER_GENVLIST="${PARALLEL_SERVER_GENVLIST},HOME,USER"
+
 # Create full paths to mw_smpd/mw_mpiexec if needed
 FULL_SMPD=${PARALLEL_SERVER_CMR:+${PARALLEL_SERVER_CMR}/bin/}mw_smpd
 FULL_MPIEXEC=${PARALLEL_SERVER_CMR:+${PARALLEL_SERVER_CMR}/bin/}mw_mpiexec
@@ -102,11 +105,13 @@ launchSmpds() {
 
 runMpiexec() {
 
-    ENVS_TO_FORWARD="PARALLEL_SERVER_DECODE_FUNCTION,PARALLEL_SERVER_STORAGE_LOCATION,PARALLEL_SERVER_STORAGE_CONSTRUCTOR,PARALLEL_SERVER_JOB_LOCATION,PARALLEL_SERVER_DEBUG,PARALLEL_SERVER_LICENSE_NUMBER,MLM_WEB_LICENSE,MLM_WEB_USER_CRED,MLM_WEB_ID"
-    LEGACY_ENVS_TO_FORWARD="MDCE_DECODE_FUNCTION,MDCE_STORAGE_LOCATION,MDCE_STORAGE_CONSTRUCTOR,MDCE_JOB_LOCATION,MDCE_DEBUG,MDCE_LICENSE_NUMBER"
-    CMD="\"${FULL_MPIEXEC}\" -smpd -phrase MATLAB -port ${SMPD_PORT} \
-        -l ${MACHINE_ARG} -genvlist $ENVS_TO_FORWARD,$LEGACY_ENVS_TO_FORWARD \
-        \"${PARALLEL_SERVER_MATLAB_EXE}\" ${PARALLEL_SERVER_MATLAB_ARGS}"
+    CMD="\"${FULL_MPIEXEC}\" -smpd \
+        -phrase MATLAB \
+        -port ${SMPD_PORT} \
+        -l ${MACHINE_ARG} \
+        -genvlist $PARALLEL_SERVER_GENVLIST \
+        \"${PARALLEL_SERVER_MATLAB_EXE}\" \
+        ${PARALLEL_SERVER_MATLAB_ARGS}"
 
     # As a debug stage: echo the command line...
     echo $CMD

communicatingSubmitFcn.m

@@ -6,7 +6,7 @@ function communicatingSubmitFcn(cluster, job, environmentProperties)
 %
 % See also parallel.cluster.generic.communicatingDecodeFcn.
 
-% Copyright 2010-2023 The MathWorks, Inc.
+% Copyright 2010-2024 The MathWorks, Inc.
 
 % Store the current filename for the errors, warnings and dctSchedulerMessages.
 currFilename = mfilename;
@@ -78,7 +78,8 @@ function communicatingSubmitFcn(cluster, job, environmentProperties)
         storageLocation = [storageLocation, fileSeparator];
     end
 end
-variables = {'PARALLEL_SERVER_DECODE_FUNCTION', decodeFunction; ...
+variables = { ...
+    'PARALLEL_SERVER_DECODE_FUNCTION', decodeFunction; ...
     'PARALLEL_SERVER_STORAGE_CONSTRUCTOR', environmentProperties.StorageConstructor; ...
     'PARALLEL_SERVER_JOB_LOCATION', environmentProperties.JobLocation; ...
     'PARALLEL_SERVER_MATLAB_EXE', environmentProperties.MatlabExecutable; ...
@@ -99,6 +100,9 @@ function communicatingSubmitFcn(cluster, job, environmentProperties)
 % Trim the environment variables of empty values.
 nonEmptyValues = cellfun(@(x) ~isempty(strtrim(x)), variables(:,2));
 variables = variables(nonEmptyValues, :);
+% List of all the variables to forward through mpiexec to the workers
+variables = [variables; ...
+    {'PARALLEL_SERVER_GENVLIST', strjoin(variables(:,1), ',')}];
 
 % The job directory as accessed by this machine
 localJobDirectory = cluster.getJobFolder(job);

getJobStateFcn.m

@@ -4,7 +4,7 @@
 % Set your cluster's PluginScriptsLocation to the parent folder of this
 % function to run it when you query the state of a job.
 
-% Copyright 2010-2022 The MathWorks, Inc.
+% Copyright 2010-2024 The MathWorks, Inc.
 
 % Store the current filename for the errors, warnings and
 % dctSchedulerMessages
@@ -62,18 +62,20 @@
 clusterState = iExtractJobState(cmdOut, schedulerIDs);
 dctSchedulerMessage(6, '%s: State %s was extracted from cluster output.', currFilename, clusterState);
 
-% If we could determine the cluster's state, we'll use that, otherwise
-% stick with MATLAB's job state.
+% If we could determine the cluster's state, we'll use that. Otherwise, we assume
+% the scheduler is no longer tracking the job because the job has terminated.
 if ~strcmp(clusterState, 'unknown')
     state = clusterState;
+else
+    state = 'finished';
 end
 
 if ~cluster.HasSharedFilesystem
-    % Decide what to do with mirroring based on the cluster's version of job state and whether or not
-    % the job is currently being mirrored:
+    % Decide what to do with mirroring based on the cluster's version of job
+    % state and whether or not the job is currently being mirrored:
     % If job is not being mirrored, and job is not finished, resume the mirror
     % If job is not being mirrored, and job is finished, do the last mirror
-    % If the job is being mirrored, and job is finished, do the last mirror.
+    % If the job is being mirrored, and job is finished, do the last mirror
     % Otherwise (if job is not finished, and we are mirroring), do nothing
     remoteConnection = getRemoteConnection(cluster);
     isBeingMirrored = remoteConnection.isJobUsingConnection(job.ID);

independentJobWrapper.sh

@@ -5,7 +5,7 @@
 # PARALLEL_SERVER_MATLAB_EXE  - the MATLAB executable to use
 # PARALLEL_SERVER_MATLAB_ARGS - the MATLAB args to use
 
-# Copyright 2010-2022 The MathWorks, Inc.
+# Copyright 2010-2024 The MathWorks, Inc.
 
 # If PARALLEL_SERVER_ environment variables are not set, assign any
 # available values with form MDCE_ for backwards compatibility

independentSubmitFcn.m

@@ -85,7 +85,8 @@ function independentSubmitFcn(cluster, job, environmentProperties)
         storageLocation = [storageLocation, fileSeparator];
     end
 end
-variables = {'PARALLEL_SERVER_DECODE_FUNCTION', decodeFunction; ...
+variables = { ...
+    'PARALLEL_SERVER_DECODE_FUNCTION', decodeFunction; ...
     'PARALLEL_SERVER_STORAGE_CONSTRUCTOR', environmentProperties.StorageConstructor; ...
     'PARALLEL_SERVER_JOB_LOCATION', environmentProperties.JobLocation; ...
     'PARALLEL_SERVER_MATLAB_EXE', environmentProperties.MatlabExecutable; ...

private/createSubmitScript.m

@@ -2,7 +2,7 @@ function createSubmitScript(outputFilename, jobName, quotedLogFile, ...
     quotedWrapperPath, additionalSubmitArgs, jobArrayString)
 % Create a script that runs the Grid Engine qsub command.
 
-% Copyright 2010-2023 The MathWorks, Inc.
+% Copyright 2010-2024 The MathWorks, Inc.
 
 if nargin < 6
     jobArrayString = [];

private/getRemoteConnection.m

@@ -4,7 +4,7 @@
 % getRemoteConnection will either retrieve a RemoteClusterAccess from the
 % cluster's UserData or it will create a new RemoteClusterAccess.
 
-% Copyright 2010-2023 The MathWorks, Inc.
+% Copyright 2010-2024 The MathWorks, Inc.
 
 % Store the current filename for the dctSchedulerMessages
 currFilename = mfilename;
@@ -70,7 +70,7 @@
                     ~strcmpi(remoteConnection.Hostname, clusterHost)
                 % The connection stored in the user data does not match the cluster host requested
                 warning('parallelexamples:GenericGridEngine:DifferentRemoteParameters', ...
-                    ['The current cluster is already using cluster host.\n', ...
+                    ['The current cluster is already using cluster host %s.\n', ...
                     'The existing connection to %s will be replaced.'], ...
                     remoteConnection.Hostname, remoteConnection.Hostname);
                 cluster.UserData.RemoteConnection = [];
@@ -123,7 +123,7 @@
 %                             (true/false).
 
 % Use the UI for prompts if MATLAB has been started with the desktop enabled
-useUI = desktop('-inuse');
+useUI = iShouldUseUI();
 username = iGetUsername(cluster, useUI);
 
 % Decide which authentication mode to use
@@ -192,6 +192,17 @@
 
 end
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function useUI = iShouldUseUI()
+if verLessThan('matlab', '9.11')
+    % Prior to R2021b, check for Java AWT components
+    useUI = isempty(javachk('awt'));
+else
+    % From R2021b onwards, can use the desktop function
+    useUI = desktop('-inuse');
+end
+end
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 function username = iGetUsername(cluster, useUI)
 
@@ -217,7 +228,8 @@
 end
 
 % useUI == false
-username = input(sprintf('Enter the username for %s:\n', cluster.AdditionalProperties.ClusterHost), 's');
+msg = sprintf('Enter the username for %s:\n ', cluster.AdditionalProperties.ClusterHost);
+username = input(msg, 's');
 
 end
 
@@ -244,7 +256,7 @@
 
 % useUI == false
 validYesNoResponse = {'y', 'n'};
-passphraseMessage = 'Does the identity file require a password? (y or n)\n';
+passphraseMessage = sprintf('Does the identity file require a password? (y or n)\n ');
 passphraseResponse = iLoopUntilValidStringInput(passphraseMessage, validYesNoResponse);
 identityFileHasPassphrase = strcmpi(passphraseResponse, 'y');
 
@@ -269,7 +281,8 @@
         end
         identityFile = fullfile(pathname, filename);
     else
-        identityFile = input(sprintf('Please enter the full path to the Identity File to use:\n'), 's');
+        msg = sprintf('Please enter the full path to the Identity File to use:\n ');
+        identityFile = input(msg, 's');
     end
 end
 
@@ -293,7 +306,7 @@
 else
     validResponses = {'1', '2', '3'};
     displayItems = [validResponses; options];
-    identityFileMessage = [promptMessage, newline, sprintf('%s) %s\n', displayItems{:})];
+    identityFileMessage = [promptMessage, newline, sprintf('%s) %s\n', displayItems{:}), ' '];
     response = iLoopUntilValidStringInput(identityFileMessage, validResponses);
     switch response
         case '1'