Hi, I'm having a strange issue with Openmpi-1.4. Whenever I try to run a program with number of mpi more than 1, it crashes.
For instance the following code: mpirun -np 2 -bynode `which relion_refine_mpi` --gpu --tau2_fudge 2 --scale --dont_combine_weights_via_disc --iter 25 --norm --psi_step 10.0 --ctf --offset_range 5.0 --oversampling 1 --pool 3 --o Runs/000757_ProtRelionClassify2D/extra/relion --i Runs/000757_ProtRelionClassify2D/input_particles.star --particle_diameter 282 --K 50 --preread_images --flatten_solvent --zero_mask --offset_step 2.0 --angpix 1.89 --j 5 Is giving me: -------------------------------------------------------------------------- 00110: It looks like opal_init failed for some reason; your parallel process is 00111: likely to abort. There are many reasons that a parallel process can 00112: fail during opal_init; some of which are due to configuration or 00113: environment problems. This failure appears to be an internal failure; 00114: here's some additional information (which may only be relevant to an 00115: Open MPI developer): 00116: 00117: opal_shmem_base_select failed 00118: --> Returned value -1 instead of OPAL_SUCCESS 00119: -------------------------------------------------------------------------- But, if I use following code, it would run fine: relion_refine --gpu --tau2_fudge 2 --scale --dont_combine_weights_via_disc --iter 25 --norm --psi_step 10.0 --ctf --offset_range 5.0 --oversampling 1 --pool 3 --o Runs/000757_ProtRelionClassify2D/extra/relion --i Runs/000757_ProtRelionClassify2D/input_particles.star --particle_diameter 282 --K 50 --preread_images --flatten_solvent --zero_mask --offset_step 2.0 --angpix 1.89 --j 5 I have used Openmpi perfectly with the same program earlier. Can't figure out what is wrong this time. Please help me out. Thank you. -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*
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