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Using slurm for langevin concurrent runs #1611

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Merged
danv61 merged 59 commits into from
Dec 23, 2025
+2,056 −172
Merged

Using slurm for langevin concurrent runs #1611

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eb794d6
stub for batch execution for langevin
danv61 Jun 10, 2025
0406ca5
WIP sample slurm script for batch execution
danv61 Jun 12, 2025
ddf58ed
WIP sample slurm script for batch execution
danv61 Jun 12, 2025
c4e8760
WIP slurm script for batch execution
danv61 Jun 12, 2025
b21fbbf
WIP: partial placeholders for batch work
jcschaff Jun 18, 2025
e4dacf9
making the directory structure for testing, mapping between windows a…
danv61 Jun 23, 2025
73b784e
WIP - coarse version of early test
danv61 Jun 23, 2025
734027b
WIP - better test, partialy runs. does not use slurm
danv61 Jun 23, 2025
2c96611
WIP
danv61 Jun 25, 2025
b3d2277
WIP - simplified testing script that somewhat runs using slurm
danv61 Jun 25, 2025
492dfcf
WIP
danv61 Jun 27, 2025
23c97e5
WIP - documentation work
danv61 Jul 1, 2025
a236e5e
Model for multi-run test, multiple-run parameters used by slurm in .x…
danv61 Jul 15, 2025
adf2b86
WIP: multiple runs - sequentially
danv61 Jul 16, 2025
be42a20
Multiple runs in parallel - proof of concept
danv61 Jul 16, 2025
80dc08a
WIP - the real test, still a work in progress
danv61 Jul 24, 2025
02ccb69
good: the testing platform, containers running under slurm
danv61 Jul 24, 2025
571f0c2
correct location of some IDA test files
danv61 Jul 24, 2025
b84f95d
WIP, moved the branch up
danv61 Sep 9, 2025
55c5a88
refactoring the langevin options panel for number of jobs and concurr…
danv61 Sep 26, 2025
7cd5bfb
total number of jobs and max number of concurrent jobs
danv61 Sep 30, 2025
ca8a9c8
total number of jobs and max number of concurrent jobs
danv61 Sep 30, 2025
eacc4ad
WIP - building slurm batch script string
danv61 Oct 6, 2025
cf1854a
building slurm batch script string, generating template slurm batch file
danv61 Oct 10, 2025
81d0ea5
template slurm batch file for testing, recovering work directory from…
danv61 Oct 15, 2025
19314a0
compute slurm job timeout based on task timeout, total num tasks, num…
danv61 Oct 16, 2025
2e382fd
additions to readme.md
danv61 Oct 31, 2025
ed0ff80
slurm script runnable from command line
danv61 Nov 5, 2025
5b4b826
slurm script runnable from command line
danv61 Nov 7, 2025
2f5be06
using here-doccument to comment out solver calls for debugging log is…
danv61 Nov 10, 2025
5028a27
this works, with set +e
danv61 Nov 13, 2025
2c7cf03
working production script
danv61 Nov 14, 2025
75c0756
building the script at runtime
danv61 Nov 17, 2025
97b0d64
building the script at runtime, verify identity with manually created…
danv61 Nov 20, 2025
97501ec
script for testing communication with the messaging server (REST API)
danv61 Dec 2, 2025
54e0cdb
script for testing communication with the messaging server (REST API)
danv61 Dec 5, 2025
d54f8b5
alpha candidate for the langevin batch slurm script creation
danv61 Dec 5, 2025
22f8f98
alpha candidate for the langevin batch slurm script creation
danv61 Dec 5, 2025
1fe31c8
alternate repository for javax.media:jai_core:1.1.3
danv61 Dec 8, 2025
84aee67
also fix dependency coordinates in vcell-core
danv61 Dec 8, 2025
8da1567
fixed xalan conflict: 2.7.3 in vcell, and 2.7.2 in bioformats
danv61 Dec 8, 2025
6178b3d
fixed jai-codec missing
danv61 Dec 8, 2025
1d738d0
align osgi annotations
danv61 Dec 8, 2025
5a68a4b
align osgi resources
danv61 Dec 8, 2025
1fdf372
align bnd resources
danv61 Dec 8, 2025
b9b931a
trying exclusion for not runtime dependencies
danv61 Dec 9, 2025
5b79529
exclusions unavailable, revert
danv61 Dec 9, 2025
117f89e
jvnet-parent
danv61 Dec 9, 2025
f808203
more dependencyManagement
danv61 Dec 9, 2025
36ba581
aligning with master
danv61 Dec 9, 2025
868fc8f
aligning with master and vcell-core pom.xml
danv61 Dec 9, 2025
bb04a5f
fixes for SlurmProxyTest
danv61 Dec 10, 2025
3617f2d
fixes for SlurmProxyTest
danv61 Dec 11, 2025
5fd263d
Merge remote-tracking branch 'origin/master' into dan-ss-slurm
danv61 Dec 11, 2025
9abce10
skip tests if external db is down
danv61 Dec 17, 2025
a3e943e
skip tests if external db is down
danv61 Dec 19, 2025
242f3a7
updated to the most recent langevin solver version
danv61 Dec 22, 2025
5497d6a
fixes messaging bug when local server
danv61 Dec 22, 2025
b523fee
Merge remote-tracking branch 'origin/master' into dan-ss-slurm
danv61 Dec 22, 2025
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6 changes: 3 additions & 3 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -191,9 +191,9 @@
<solvers-vcell-mac.version>v0.0.44-dev4</solvers-vcell-mac.version>
<solvers-vcell-windows.version>v0.0.40</solvers-vcell-windows.version>
<solvers-vcell-linux.version>v0.0.44-dev4</solvers-vcell-linux.version>
<solvers-langevin-mac.version>1.4.4</solvers-langevin-mac.version>
<solvers-langevin-windows.version>1.4.4</solvers-langevin-windows.version>
<solvers-langevin-linux.version>1.4.4</solvers-langevin-linux.version>
<solvers-langevin-mac.version>1.4.5</solvers-langevin-mac.version>
<solvers-langevin-windows.version>1.4.5</solvers-langevin-windows.version>
<solvers-langevin-linux.version>1.4.5</solvers-langevin-linux.version>
</properties>


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2 changes: 1 addition & 1 deletion vcell-apiclient/src/main/java/org/vcell/api/server/AsynchMessageManager.java
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@CodeByDrescher CodeByDrescher Dec 23, 2025

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Asked Dan to warn development chat on slack this is coming in, because fix has not yet been merged

Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ public AsynchMessageManager(ClientServerManager csm) {
* no-op if already called
*/
public synchronized void startPolling() {
if (!bPoll.get()) {
if (!bPoll.get() && !clientServerManager.isVCellClientDevMain()) {
bPoll.set(true);
if (executorService == null) {
executorService = VCellExecutorService.get();
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6 changes: 5 additions & 1 deletion vcell-apiclient/src/main/java/org/vcell/api/server/ClientServerManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,11 @@ public class ClientServerManager implements ClientServerInterface {
private final static Logger lg = LogManager.getLogger(ClientServerManager.class);
private final VCellConnectionFactory vcellConnectionFactory;
public final Auth0ConnectionUtils auth0ConnectionUtils;


public boolean isVCellClientDevMain() {
return !(vcellConnectionFactory instanceof RemoteProxyVCellConnectionFactory);
}

public interface InteractiveContextDefaultProvider {
InteractiveClientServerContext getInteractiveContext();
}
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