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November 30, 2018 18:50
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abyss-pe mpirun='mpirun --mca btl sm' v=-v k=96 np=24 name=DjPG2103 lr='lra' lra=. | |
./data/barcoded.fastq | |
mpirun --mca btl sm -np 24 ABYSS-P -k96 -q3 -v --coverage-hist=coverage.hist -s DjPG2103-bubbles.fa -o DjPG2103-1.fa ../data/barcoded.fastq | |
-------------------------------------------------------------------------- | |
At least one pair of MPI processes are unable to reach each other for | |
MPI communications. This means that no Open MPI device has indicated | |
that it can be used to communicate between these processes. This is | |
an error; Open MPI requires that all MPI processes be able to reach | |
each other. This error can sometimes be the result of forgetting to | |
specify the "self" BTL. | |
Process 1 ([[35387,1],13]) is on host: oak | |
Process 2 ([[35387,1],13]) is on host: oak | |
BTLs attempted: sm | |
Your MPI job is now going to abort; sorry. | |
-------------------------------------------------------------------------- | |
[oak:15890] *** An error occurred in MPI_Init | |
[oak:15890] *** on a NULL communicator | |
[oak:15890] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15890] *** and potentially your MPI job) | |
[oak:15893] *** An error occurred in MPI_Init | |
[oak:15893] *** on a NULL communicator | |
[oak:15893] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15893] *** and potentially your MPI job) | |
[oak:15904] *** An error occurred in MPI_Init | |
[oak:15904] *** on a NULL communicator | |
[oak:15904] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15904] *** and potentially your MPI job) | |
[oak:15843] *** An error occurred in MPI_Init | |
[oak:15843] *** on a NULL communicator | |
[oak:15843] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15843] *** and potentially your MPI job) | |
[oak:15845] *** An error occurred in MPI_Init | |
[oak:15845] *** on a NULL communicator | |
[oak:15845] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15845] *** and potentially your MPI job) | |
[oak:15846] *** An error occurred in MPI_Init | |
[oak:15846] *** on a NULL communicator | |
[oak:15846] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15846] *** and potentially your MPI job) | |
[oak:15853] *** An error occurred in MPI_Init | |
[oak:15853] *** on a NULL communicator | |
[oak:15853] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15853] *** and potentially your MPI job) | |
[oak:15857] *** An error occurred in MPI_Init | |
[oak:15857] *** on a NULL communicator | |
[oak:15857] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15857] *** and potentially your MPI job) | |
[oak:15863] *** An error occurred in MPI_Init | |
[oak:15863] *** on a NULL communicator | |
[oak:15863] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15863] *** and potentially your MPI job) | |
[oak:15866] *** An error occurred in MPI_Init | |
[oak:15866] *** on a NULL communicator | |
[oak:15866] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15866] *** and potentially your MPI job) | |
[oak:15869] *** An error occurred in MPI_Init | |
[oak:15869] *** on a NULL communicator | |
[oak:15869] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15869] *** and potentially your MPI job) | |
[oak:15870] *** An error occurred in MPI_Init | |
[oak:15870] *** on a NULL communicator | |
[oak:15870] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15870] *** and potentially your MPI job) | |
[oak:15872] *** An error occurred in MPI_Init | |
[oak:15872] *** on a NULL communicator | |
[oak:15872] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15872] *** and potentially your MPI job) | |
[oak:15877] *** An error occurred in MPI_Init | |
[oak:15877] *** on a NULL communicator | |
[oak:15877] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15877] *** and potentially your MPI job) | |
[oak:15880] *** An error occurred in MPI_Init | |
[oak:15880] *** on a NULL communicator | |
[oak:15880] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15880] *** and potentially your MPI job) | |
[oak:15885] *** An error occurred in MPI_Init | |
[oak:15885] *** on a NULL communicator | |
[oak:15885] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15885] *** and potentially your MPI job) | |
[oak:15887] *** An error occurred in MPI_Init | |
[oak:15887] *** on a NULL communicator | |
[oak:15887] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15887] *** and potentially your MPI job) | |
[oak:15899] *** An error occurred in MPI_Init | |
[oak:15899] *** on a NULL communicator | |
[oak:15899] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15899] *** and potentially your MPI job) | |
[oak:15907] *** An error occurred in MPI_Init | |
[oak:15907] *** on a NULL communicator | |
[oak:15907] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15907] *** and potentially your MPI job) | |
-------------------------------------------------------------------------- | |
MPI_INIT has failed because at least one MPI process is unreachable | |
from another. This *usually* means that an underlying communication | |
plugin -- such as a BTL or an MTL -- has either not loaded or not | |
allowed itself to be used. Your MPI job will now abort. | |
You may wish to try to narrow down the problem; | |
* Check the output of ompi_info to see which BTL/MTL plugins are | |
available. | |
* Run your application with MPI_THREAD_SINGLE. | |
* Set the MCA parameter btl_base_verbose to 100 (or mtl_base_verbose, | |
if using MTL-based communications) to see exactly which | |
communication plugins were considered and/or discarded. | |
-------------------------------------------------------------------------- | |
[oak:15842] *** An error occurred in MPI_Init | |
[oak:15842] *** on a NULL communicator | |
[oak:15842] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15842] *** and potentially your MPI job) | |
[oak:15847] *** An error occurred in MPI_Init | |
[oak:15847] *** on a NULL communicator | |
[oak:15847] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15847] *** and potentially your MPI job) | |
[oak:15851] *** An error occurred in MPI_Init | |
[oak:15851] *** on a NULL communicator | |
[oak:15851] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15851] *** and potentially your MPI job) | |
[oak:15874] *** An error occurred in MPI_Init | |
[oak:15874] *** on a NULL communicator | |
[oak:15874] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15874] *** and potentially your MPI job) | |
[oak:15844] *** An error occurred in MPI_Init | |
[oak:15844] *** on a NULL communicator | |
[oak:15844] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, | |
[oak:15844] *** and potentially your MPI job) | |
[oak:15836] 23 more processes have sent help message help-mca-bml-r2.txt / unreachable proc | |
[oak:15836] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages | |
[oak:15836] 23 more processes have sent help message help-mpi-runtime.txt / mpi_init:startup:pml-add-procs-fail | |
make: *** [/s/chopin/a/grad/asharifi/usr/bin/bin/abyss-pe:548: DjPG2103-1.fa] Error 1 |
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