Oswin,
unfortunatly some important info is missing. i guess the root cause is Open MPI was not configure'd with --enable-debugcould you please update your torque script and simply add the following snippet before invoking mpirun
echo PBS_NODEFILE cat $PBS_NODEFILE echo ---as i wrote in an other email, i suspect hosts are not ordered (and i'd like to confirm that) and Open MPI does not handle that correctly
Cheers, Gilles On 9/7/2016 10:25 PM, Oswin Krause wrote:
Hi Gilles,Thanks for the hint with the machinefile. I know it is not equivalent and i do not intend to use that approach. I just wanted to know whether I could start the program successfully at all.Outside torque(4.2), rsh seems to be used which works fine, querying a password if no kerberos ticket is thereHere is the output: [zbh251@a00551 ~]$ mpirun -V mpirun (Open MPI) 2.0.1 [zbh251@a00551 ~]$ ompi_info | grep rasMCA ras: loadleveler (MCA v2.1.0, API v2.0.0, Component v2.0.1) MCA ras: simulator (MCA v2.1.0, API v2.0.0, Component v2.0.1) MCA ras: slurm (MCA v2.1.0, API v2.0.0, Component v2.0.1)MCA ras: tm (MCA v2.1.0, API v2.0.0, Component v2.0.1)[zbh251@a00551 ~]$ mpirun --mca plm_base_verbose 10 --tag-output -display-map hostname [a00551.science.domain:04104] mca: base: components_register: registering framework plm components [a00551.science.domain:04104] mca: base: components_register: found loaded component isolated [a00551.science.domain:04104] mca: base: components_register: component isolated has no register or open function [a00551.science.domain:04104] mca: base: components_register: found loaded component rsh [a00551.science.domain:04104] mca: base: components_register: component rsh register function successful [a00551.science.domain:04104] mca: base: components_register: found loaded component slurm [a00551.science.domain:04104] mca: base: components_register: component slurm register function successful [a00551.science.domain:04104] mca: base: components_register: found loaded component tm [a00551.science.domain:04104] mca: base: components_register: component tm register function successful [a00551.science.domain:04104] mca: base: components_open: opening plm components [a00551.science.domain:04104] mca: base: components_open: found loaded component isolated [a00551.science.domain:04104] mca: base: components_open: component isolated open function successful [a00551.science.domain:04104] mca: base: components_open: found loaded component rsh [a00551.science.domain:04104] mca: base: components_open: component rsh open function successful [a00551.science.domain:04104] mca: base: components_open: found loaded component slurm [a00551.science.domain:04104] mca: base: components_open: component slurm open function successful [a00551.science.domain:04104] mca: base: components_open: found loaded component tm [a00551.science.domain:04104] mca: base: components_open: component tm open function successful [a00551.science.domain:04104] mca:base:select: Auto-selecting plm components [a00551.science.domain:04104] mca:base:select:( plm) Querying component [isolated] [a00551.science.domain:04104] mca:base:select:( plm) Query of component [isolated] set priority to 0 [a00551.science.domain:04104] mca:base:select:( plm) Querying component [rsh] [a00551.science.domain:04104] mca:base:select:( plm) Query of component [rsh] set priority to 10 [a00551.science.domain:04104] mca:base:select:( plm) Querying component [slurm] [a00551.science.domain:04104] mca:base:select:( plm) Querying component [tm] [a00551.science.domain:04104] mca:base:select:( plm) Query of component [tm] set priority to 75 [a00551.science.domain:04104] mca:base:select:( plm) Selected component [tm][a00551.science.domain:04104] mca: base: close: component isolated closed[a00551.science.domain:04104] mca: base: close: unloading component isolated[a00551.science.domain:04104] mca: base: close: component rsh closed [a00551.science.domain:04104] mca: base: close: unloading component rsh [a00551.science.domain:04104] mca: base: close: component slurm closed [a00551.science.domain:04104] mca: base: close: unloading component slurm[a00551.science.domain:04109] mca: base: components_register: registering framework plm components [a00551.science.domain:04109] mca: base: components_register: found loaded component rsh [a00551.science.domain:04109] mca: base: components_register: component rsh register function successful [a00551.science.domain:04109] mca: base: components_open: opening plm components [a00551.science.domain:04109] mca: base: components_open: found loaded component rsh [a00551.science.domain:04109] mca: base: components_open: component rsh open function successful [a00551.science.domain:04109] mca:base:select: Auto-selecting plm components [a00551.science.domain:04109] mca:base:select:( plm) Querying component [rsh] [a00551.science.domain:04109] mca:base:select:( plm) Query of component [rsh] set priority to 10 [a00551.science.domain:04109] mca:base:select:( plm) Selected component [rsh] [a00551.science.domain:04109] [[53688,0],1] bind() failed on error Address already in use (98) [a00551.science.domain:04109] [[53688,0],1] ORTE_ERROR_LOG: Error in file oob_usock_component.c at line 228Data for JOB [53688,1] offset 0 ======================== JOB MAP ======================== Data for node: a00551 Num slots: 2 Max slots: 0 Num procs: 2Process OMPI jobid: [53688,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] Process OMPI jobid: [53688,1] App: 0 Process rank: 1 Bound: socket 1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt 0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket 1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt 0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt 0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB]Data for node: a00553.science.domain Num slots: 1 Max slots: 0 Num procs: 1 Process OMPI jobid: [53688,1] App: 0 Process rank: 2 Bound: socket 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..]=============================================================[a00551.science.domain:04104] [[53688,0],0] complete_setup on job [53688,1] [a00551.science.domain:04104] [[53688,0],0] plm:base:receive update proc state command from [[53688,0],1] [a00551.science.domain:04104] [[53688,0],0] plm:base:receive got update_proc_state for job [53688,1][1,0]<stdout>:a00551.science.domain [1,2]<stdout>:a00551.science.domain[a00551.science.domain:04104] [[53688,0],0] plm:base:receive update proc state command from [[53688,0],1] [a00551.science.domain:04104] [[53688,0],0] plm:base:receive got update_proc_state for job [53688,1][1,1]<stdout>:a00551.science.domain [a00551.science.domain:04109] mca: base: close: component rsh closed [a00551.science.domain:04109] mca: base: close: unloading component rsh [a00551.science.domain:04104] mca: base: close: component tm closed [a00551.science.domain:04104] mca: base: close: unloading component tm On 2016-09-07 14:41, Gilles Gouaillardet wrote:Hi, Which version of Open MPI are you running ? I noted that though you are asking three nodes and one task per node, you have been allocated 2 nodes only. I do not know if this is related to this issue. Note if you use the machinefile, a00551 has two slots (since it appears twice in the machinefile) but a00553 has 20 slots (since it appears once in the machinefile, the number of slots is automatically detected) Can you run mpirun --mca plm_base_verbose 10 ... So we can confirm tm is used.Before invoking mpirun, you might want to cleanup the ompi directory in /tmpCheers, Gilles Oswin Krause <oswin.kra...@ruhr-uni-bochum.de> wrote:Hi,I am currently trying to set up OpenMPI in torque. OpenMPI is build withtm support. Torque is correctly assigning nodes and I can run mpi-programs on single nodes just fine. the problem starts when processes are split between nodes. For example, I create an interactive session with torque and start a program by qsub -I -n -l nodes=3:ppn=1 mpirun --tag-output -display-map hostname which leads to [a00551.science.domain:15932] [[65415,0],1] bind() failed on error Address already in use (98) [a00551.science.domain:15932] [[65415,0],1] ORTE_ERROR_LOG: Error in file oob_usock_component.c at line 228 Data for JOB [65415,1] offset 0 ======================== JOB MAP ======================== Data for node: a00551 Num slots: 2 Max slots: 0 Num procs: 2 Process OMPI jobid: [65415,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] Process OMPI jobid: [65415,1] App: 0 Process rank: 1 Bound: socket 1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt 0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket 1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt 0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt 0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB]Data for node: a00553.science.domain Num slots: 1 Max slots: 0 Numprocs: 1 Process OMPI jobid: [65415,1] App: 0 Process rank: 2 Bound: socket 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] ============================================================= [1,0]<stdout>:a00551.science.domain [1,2]<stdout>:a00551.science.domain [1,1]<stdout>:a00551.science.domain if I login on a00551 and start using the hostfile generated by the PBS_NODEFILE, everything works: (from within the interactive session) echo $PBS_NODEFILE /var/lib/torque/aux//278.a00552.science.domain cat $PBS_NODEFILE a00551.science.domain a00553.science.domain a00551.science.domain (from within the separate login) mpirun --hostfile /var/lib/torque/aux//278.a00552.science.domain -np 3 --tag-output -display-map hostname Data for JOB [65445,1] offset 0 ======================== JOB MAP ======================== Data for node: a00551 Num slots: 2 Max slots: 0 Num procs: 2 Process OMPI jobid: [65445,1] App: 0 Process rank: 0 Bound: socket 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] Process OMPI jobid: [65445,1] App: 0 Process rank: 1 Bound: socket 1[core 10[hwt 0-1]], socket 1[core 11[hwt 0-1]], socket 1[core 12[hwt 0-1]], socket 1[core 13[hwt 0-1]], socket 1[core 14[hwt 0-1]], socket 1[core 15[hwt 0-1]], socket 1[core 16[hwt 0-1]], socket 1[core 17[hwt 0-1]], socket 1[core 18[hwt 0-1]], socket 1[core 19[hwt 0-1]]:[../../../../../../../../../..][BB/BB/BB/BB/BB/BB/BB/BB/BB/BB]Data for node: a00553.science.domain Num slots: 20 Max slots: 0 Numprocs: 1 Process OMPI jobid: [65445,1] App: 0 Process rank: 2 Bound: socket 0[core 0[hwt 0-1]], socket 0[core 1[hwt 0-1]], socket 0[core 2[hwt 0-1]], socket 0[core 3[hwt 0-1]], socket 0[core 4[hwt 0-1]], socket 0[core 5[hwt 0-1]], socket 0[core 6[hwt 0-1]], socket 0[core 7[hwt 0-1]], socket 0[core 8[hwt 0-1]], socket 0[core 9[hwt 0-1]]:[BB/BB/BB/BB/BB/BB/BB/BB/BB/BB][../../../../../../../../../..] ============================================================= [1,0]<stdout>:a00551.science.domain [1,2]<stdout>:a00553.science.domain [1,1]<stdout>:a00551.science.domain I am kind of lost whats going on here. Anyone having an idea? I am seriously considering this to be the problem of kerberos authentification that we have to work with, but I fail to see how this should affect the sockets. Best, Oswin _______________________________________________ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users_______________________________________________ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users_______________________________________________ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users
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