Re: Problem with mpi abyss-pe execution

[Tony Raymond]

Hi Friman,

Don't use the mpirun command. abyss-pe will call mpirun when it needs to.

Cheers,

Tony

On 2013-02-05, at 11:11 AM, <fsanch...@gmail.com> <fsanch...@gmail.com> wrote:

Dear all,

I am having a problem executing mpi abyss version. The command I use for the execution is like this:

mpirun /path_of_abyss_binaries/abyss-pe name=my_test np=4 c=10 k=63 in='/path_to_my_fastq_files/file_R1.fastq /path_to_my_fastq_files/file_R2.fastq'

After executing this line I have the following output:

make: Nothing to be done for `/path_to_my_fastq_files/file_R1.fastq /path_to_my_fastq_files/file_R2.fastq'.

make: Nothing to be done for `/path_to_my_fastq_files/file_R1.fastq /path_to_my_fastq_files/file_R2.fastq'.

make: Nothing to be done for `/path_to_my_fastq_files/file_R1.fastq /path_to_my_fastq_files/file_R2.fastq'.

make: Nothing to be done for `/path_to_my_fastq_files/file_R1.fastq /path_to_my_fastq_files/file_R2.fastq'.

It seems like abyss-pe is not taking the second fastq file as another input. 

I have tried things like putting the input in a environtment variable, like this:

export in='/path_to_my_pe_fastq_files/file_R1.fastq /path_to_my_pe_fastq_files/file_R2.fastq'

But it did not work.

I am using abyss-1.3.4 configure like:

cd ../build/abyss-1.3.4

../../sources/abyss-1.3.4/configure --prefix=/path_of_abyss_binaries --with-boost=//path_of_boost_1_49_0/include --enable-maxk=96 --with-mpi=/apps/INTEL/impi/4.1.0.024/intel64

What is the problem?, do you have any suggestion for solving this issue?

Thanks a lot for your help!.

Friman

--
You received this message because you are subscribed to the Google Groups "ABySS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to abyss-users...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[Friman Sánchez]

Hi Tony,

Thanks a lot for your answer!.

I have tried what you suggested. That is, my execution command now is:

/path_of_abyss_binaries/abyss-pe name=my_test np=4 c=10 k=63 in='/path_to_my_fastq_files/file_R1.fastq /path_to_my_fastq_files/file_R2.fastq'

And the previous problem did not appear again.

How ever I have this other:

mpirun.lsf: LSF_PJL_TYPE is undefined. Exit ...

make: *** [my_test-1.fa] Error 1

So, yes, I am using LSF queue system in the machine. But I do not see what would be the problem.

Now, I did my abyss configuration with:

../../sources/abyss-1.3.4/configure --prefix=/path_of_abyss_binaries/abyss-1.3.4 --with-boost=/path_of_boost_1_49_0/include --enable-maxk=96 --with-mpi=/apps/OPENMPI/1.5.4

And the config.log say:

PATH: /apps/OPENMPI/1.5.4//bin   

...

configure:6297: checking for mpi.h

configure:6297: result: yes

configure:6633: checking for MPI_Init in -lmpi

which is OK.

(Note I have changed to openmpi 1.5.4, which is the default mpi installed in my system).

I have verified that I am using the correct mpi library doing:

which /apps/OPENMPI/1.5.4/bin/mpirun

An also, ldd ABYSS-P                           

        linux-vdso.so.1 =>  (0x00007fff0a527000)

        libmpi.so.1 => /apps/OPENMPI/1.5.4//lib/libmpi.so.1 (0x00002b9295ae9000)

        libdl.so.2 => /lib64/libdl.so.2 (0x00002b9295e83000)

        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b9296087000)

        libm.so.6 => /lib64/libm.so.6 (0x00002b9296391000)

        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b929660b000)

        libc.so.6 => /lib64/libc.so.6 (0x00002b9296821000)

        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b9296b95000)

        libnsl.so.1 => /lib64/libnsl.so.1 (0x00002b9296db3000)

        libutil.so.1 => /lib64/libutil.so.1 (0x00002b9296fcb000)

        /lib64/ld-linux-x86-64.so.2 (0x00002b92958c8000)

So, I do not know what is the problem..

Do you have any suggestion?..

Thanks again.

Friman Sanchez.

[Tony Raymond]

Hi Friman,

It looks like that error is related to your job submission method. Some googling suggests you need to submit with the -a openmpi option of bsub, but  I have no way to test this…

I think your ABySS installation is fine. I may be able to help more if I knew how you were submitting this job to your queue system. Are you just running abyss-pe from the command line?

Thanks,

Tony

[Friman Sánchez]

Hi Tony,

I am executing abyss-pe through a script like this:


-------------
#!/bin/bash

# BSUB -J lanza_assemblers.cmd
# BSUB -cwd .
# BSUB -o lanza_assemblers.out
# BSUB -e lanza_assemblers.err
# BSUB -n 2
# BSUB -R"span[ptile=4]"
# BSUB -W 40:00

/home/bsc18/bsc18025/ASSEMBLERS/abyss-1.3.4/bin/abyss-pe name=my_test np=4 c=10 k=63 in='/home/bsc18/bsc18025/inputs/file_R1.fastq /home/bsc18/bsc18025/inputs/file_R2.fastq'

----------------

That is the way the system administrators suggest to send jobs to the machine. Do you see something wrong?

However I will try using the -a openmpi option on bsub.

Thanks a lot,
Friman.

[Tony Raymond]

Hi Friman,

Adding #BSUB -a openmpi to the header might work:

http://hpc-dev.cineca.it/content/what-does-message-mpirunlsf-lsfpjltype-undefined-exit-mean

Let me know if it does.

Thanks,

Tony

[Friman Sánchez]

Hi Tony, 

I added the BSUB -a openmpi option in the comand and it worked perfectly!.

Thanks a lot for your help.

Friman