FAQ Database Discussion Community


Changing priority of job in SGE using python drmaa wrapper

python,python-2.7,hpc,sungridengine,drmaa
When I try to submit a job using the python drmaa wrapper, I get a DeniedByDrmException: code 17: job rejected: positive submission priority requires operator privileges. How do I change the priority of jobs that I submit using the Python DRMAA wrapper?...

Operating in parallel on a large constant datastructure in Julia

performance,parallel-processing,julia-lang,hpc
I have a large vector of vectors of strings: There are around 50,000 vectors of strings, each of which contains 2-15 strings of length 1-20 characters. MyScoringOperation is a function which operates on a vector of strings (the datum) and returns an array of 10100 scores (as Float64s). It takes...

Is OpenCL ready for use on CPU?

opencl,mpi,cluster-computing,hpc
In the lab we have an heterogeneous cluster setup, with many Intel CPUs, a few AMD CPUs and a couple of Nvidia GPUs. For HPC development, the one thing I know that I could write once and run everywhere on this setup is OpenCL (not even Java ;) ). But...

Barrier after MPI non-blocking call, without bookkeeping?

c++,parallel-processing,mpi,cluster-computing,hpc
I'm doing a bunch of MPI_Iallreduce non-blocking communications. I've added these Iallreduce calls to several different places in my code. Every so often, I want to pause and wait for all the Iallreduce calls to finish. Version 1 with MPI_Request bookkeeping -- this works: MPI_Request requests[]; MPI_Iallreduce(..., requests[0]); ... MPI_Iallreduce(...,...

Move a range of jobs to another queue with qmove

bash,batch-processing,hpc,torque
I have several (idle) jobs scheduled on a cluster that I want to move to another queue. I can move a single job like this (where 1234 is the job id): qmove newQueue 1234 But now I have hundreds of jobs that I want to move to newQueue. Is it...

Netlogo HPC CPU Percentage Use Increase

linux,cloud,netlogo,hpc
I submit jobs using headless NetLogo to a HPC server by the following code: #!/bin/bash #$ -N r20p #$ -q all.q #$ -pe mpi 24 /home/abhishekb/netlogo/netlogo-5.1.0/netlogo-headless.sh \ --model /home/abhishekb/models/corrected-rk4-20presults.nlogo \ --experiment test \ --table /home/abhishekb/csvresults/corrected-rk4-20presults.csv Below is the snapshot of a cluster queue using: qstat -g c I wish to...

OpenMPI and rank/core bindings

mpi,openmpi,hpc
I'm having issues with OpenMPI where different MPI ranks are being repeatably bound to the same CPU cores. I'm using a server with 32 hardware cores (no hyper-threading), Ubuntu 14.04.2 LTS and OpenMPI 1.8.4, compiled with Intel compiler 15.0.1. For instance, I can run my executable with 8 MPI ranks,...

LAPACK C (mkl) dptsv row major/column major: Does it make a different for vectors

lapack,hpc,scientific-computing,intel-mkl
Folks, I'm calling LAPACKE_dptsv If all arguments are 1d arrays, does it matter if I call the data LAPACK_ROW_MAJOR or LAPACK_COL_MAJOR ?...

Modify attributes (including queue) of a pbs jobs

hpc,torque
I want to change the attributes (walltime and queue) of several (idle) jobs scheduled on a cluster. When I do (where 1234 is the job id): qalter -l walltime=24:00:00 -q newQueue 1234 I get the following error: qalter: illegally formed job identifier: newQueue What can I do?...

Running NetLogo on HPC machine: how to specify the number of cores to be used?

netlogo,hpc
$ wget https://ccl.northwestern.edu/netlogo/5.1.0/netlogo-5.1.0.tar.gz $ tar -xzf netlogo-5.1.0.tar.gz $ ~/netlogo-5.1.0/netlogo-headless.sh \ --model ~/myproject/MyModel.nlogo \ --experiment MyExperiment \ --table ~/myproject/MyNewOutputData.csv Using the above commands to run a netlogo headless on HPC machine. The problem is how to I specify the number of cores to be used or does by default take...

cannot send std::vector using MPI_Send and MPI_Recv

c++,vector,parallel-processing,mpi,hpc
I am trying to send std:vector using MPI send and recv functions but I have reached no where. I get errors like Fatal error in MPI_Recv: Invalid buffer pointer, error stack: MPI_Recv(186): MPI_Recv(buf=(nil), count=2, MPI_INT, src=0, tag=0, MPI_COMM_WORLD, status=0x7fff9e5e0c80) failed MPI_Recv(124): Null buffer pointer I tried multiple combinations A) like...

MPI Fortran WTIME not working well

parallel-processing,fortran,mpi,hpc
I am coding using Fortran MPI and I need to get the run time of the program. Therefore I tried to use the WTIME() function but I am getting some strange results. Part of the code is like this: program heat_transfer_1D_parallel implicit none include 'mpif.h' integer myid,np,rc,ierror,status(MPI_STATUS_SIZE) integer :: N,N_loc,i,k,e...