Hi,
I run a small Ray job on a cluster to check openmpi and Ray. The current versions on the cluster are openmpi-1.6.4 and Ray is 2.1.
When compiled on my server with openmpi-1.4, Ray2.1 works just fine with large metazoan dataset (about 30 GB) completing assembly in about 20 hours on machine with 2 quad core E5620 (16 threads) and 96GB memory
On the cluster Ray2.1 compiled fine as well, and then I tried to run it with one of datasets (about 36 MB) from the above pile that assembled fine on my server. It failed, generating ouput, which I am not quite understand and would appreciate help in interpretation and fixing the problem. Here is Ray.job file:
Here is Ray.conf file:
The ouput file is a bit loger, so it is attached.
I run a small Ray job on a cluster to check openmpi and Ray. The current versions on the cluster are openmpi-1.6.4 and Ray is 2.1.
When compiled on my server with openmpi-1.4, Ray2.1 works just fine with large metazoan dataset (about 30 GB) completing assembly in about 20 hours on machine with 2 quad core E5620 (16 threads) and 96GB memory
On the cluster Ray2.1 compiled fine as well, and then I tried to run it with one of datasets (about 36 MB) from the above pile that assembled fine on my server. It failed, generating ouput, which I am not quite understand and would appreciate help in interpretation and fixing the problem. Here is Ray.job file:
Code:
#$ -S /bin/bash #$ -cwd # #$ -N RayTest #$ -pe openmpi 32 #$ -l h_rt=00:10:00,s_rt=00:08:00,h_vmem=3G #$ -j y # #$ -M [email protected] #$ -m eas # # Load the appropriate module files # Should be loaded already #$ -V mpiexec -n $NSLOTS ~/bin/Ray ~/jobs/Ray/Ray.conf
Code:
# configuration file -k 31 # k-mer=31 # default autocalc averageOuterDistance standardDeviation # all reads trimmed, Q30, FGMGPGIGVA -s <TestFile.fasta> # single read file -o ~/jobs/Ray/RayOutput # outputDirectory -one-color-per-file # Sets one color per file instead of one per sequence -amos # writes the AMOS file called RayOutput/AMOS.afg #-show-memory-usage # Shows memory usage # -show-memory-allocations # Shows memory allocation events #-write-checkpoints ~/SC/Ray/Checkpoints # Write checkpoint files
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