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HyPhy: Hypothesis testing using Phylogenies
http://www.hyphy.org
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Unfinished Nex file from GARD #1565

Closed Daniyalprime closed 1 year ago

Daniyalprime commented 1 year ago

I tried to run MEME in datamonkey web server. But it is giving me the error mentioned below. I looked into the nex file ,i think it is not finished. Ticket Number : 2371889.new-silverback

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

[n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:16801] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 HYPHYMPI terminated. Error: HyPhy killed by signal 15

spond commented 1 year ago

Dear @Daniyalprime,

Can you please provide the Datamonkey URL (not the ticket number)?

Best, Sergei

Daniyalprime commented 1 year ago

Sure.Thank you for replying. https://www.datamonkey.org/gard/63d7969ec82f520f6a32b53a

stevenweaver commented 1 year ago

Dear @Daniyalprime,

It appears that my failsafe for this situation worked, and that the page is now reporting your results (as of 6AM ET this morning).

Can you please confirm that your issue is resolved?

Best, Steven

Daniyalprime commented 1 year ago

When I upload the partition file from GARD into MEME, the issue is still happening.@stevenweaver

Standard Error Message

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

[n6:86629] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:86629] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:86629] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:86629] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:86629] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:86629] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:86629] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 [n6:86629] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 1741 HYPHYMPI terminated. Error: HyPhy killed by signal 15

stevenweaver commented 1 year ago

Dear @Daniyalprime,

Thank you. I see now. We have made adjustments to the Datamonkey backend. Can you try rerunning your job?

Best, Steven

Daniyalprime commented 1 year ago

I think I fixed the problem. GARD's partition output file is incomplete (Incomplete Tree) and that's why MEME was giving that error. Thank you again for responding.