is 'mpi_bloom.h' mandatory and included?

[dbrami]

I am trying to compile for multi-cpu support using openmpi. Here is my command and the result:

dbrami@asm05.c01:/sgi/asmopt/src/facs/facs
cmd-> make mpi
Make sure you have MPI support on your cluster hint: module load openmpi
#mpicc -c *.c -O3 -Wall -g -DNODEBUG -fopenmp -D_FILE_OFFSET_BITS=64 -D_LARGE_FILE -lm -lz
#mpicc -c mpi_decon.c -O3 -D_FILE_OFFSET_BITS=64 -D_LARGE_FILE 
#mpicc -o mpi_decon mpi_decon.o bloom.o suggestions.o lookup3.o  -lm -O3 -Wall -g -DNODEBUG -fopenmp -D_FILE_OFFSET_BITS=64 -D_LARGE_FILE
mpicc -c mpi_bloom.c -O3 -Wall -g -DNODEBUG -fopenmp -D_FILE_OFFSET_BITS=64 -D_LARGE_FILE
mpi_bloom.c:25:23: error: mpi_bloom.h: No such file or directory
mpi_bloom.c:49: warning: return type defaults to ‘int’
mpi_bloom.c: In function ‘main’:
mpi_bloom.c:138: warning: implicit declaration of function ‘struc_init’
mpi_bloom.c:139: warning: implicit declaration of function ‘make_list’
mpi_bloom.c:139: warning: initialization makes pointer from integer without a cast
mpi_bloom.c:153: warning: implicit declaration of function ‘gz_mpi’
mpi_bloom.c:166: warning: ignoring #pragma omp task
mpi_bloom.c:183: warning: implicit declaration of function ‘gather’
mpi_bloom.c:186: error: too few arguments to function ‘report’
mpi_bloom.c:58: warning: unused variable ‘exit_sign’
mpi_bloom.c: At top level:
mpi_bloom.c:194: error: conflicting types for ‘struc_init’
mpi_bloom.c:138: error: previous implicit declaration of ‘struc_init’ was here
mpi_bloom.c:251: error: conflicting types for ‘gz_mpi’
mpi_bloom.c:153: error: previous implicit declaration of ‘gz_mpi’ was here
make: *** [mpi] Error 1

It seems to be complaining about a missing file 'mpi_bloom.h' that is not included in source nor in the repository. Any ideas?

[tzcoolman]

@brainstorm Very strange. I ll take care of that. My local version doesn't have mpi_bloom.h

[dbrami]

Any progress on this please? Otherwise the size of the data that needs to be filtered makes single CPU FACS unusable.

[tzcoolman]

@brainstorm i'm on it now...

[guillermo-carrasco]

hi @dbrami , could you please pull the latest master branch and try to compile again?

Thanks,

[dbrami]

I compiled again and this time successfully. But running mpi_facs does not recognize the 'n' or 'np' parameter flag for number of processors; Also, the mpi_facs does not seem to jive with the usage statement or the documentation of the usage for vanilla facs.

/sgi/asmopt/src/facs/facs/facs_mpi -n 64 -r ecoli.bloom -q 3xtest.fasta
/sgi/asmopt/src/facs/facs/facs_mpi: invalid option -- n
Unknown option: -n

I also went through the mpi_bloom.c file and looked at line 79-111 and did not find a param for number of processors

[tzcoolman]

Hi @dbrami, if you want to run facs_mpi, do it like this: mpirun -n 4 /sgi/asmopt/src/facs/facs/facs_mpi/facs_mpi -r ecoli.bloom -q 3xtest.fasta This is the standard procedure of running mpi and make sure you have either openmpi or mpich on you machine.