Problem [proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)

[T.Hamdi Kitapci]

Hi,
I am running abyss using the command:

abyss-pe -C $output_folder k=39 name="$output_folder/A_thaliana" in="$read_1 $read_2"

in the output folder I get this:

/home/tkitapci/libs/lib_for_python/anaconda2/bin/mpirun -np 16 ABYSS-P -k39 -q3   --coverage-hist=coverage.hist -s /lustre
/groups/cbi/tkitapci/A_Thaliana_data_set/Abyss/A_thaliana-bubbles.fa  -o /lustre/groups/cbi/tkitapci/A_Thaliana_data_set/Abyss/A_thaliana-1.fa /lustre/groups/cbi/tkitapci/A_Thaliana_data_set/PE_lib_SRS349086/SRR519624_1.fastq /lustre/groups/cbi/tkitapci/A_Thaliana_data_set/PE_lib_SRS349086/SRR519624_2.fastq
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)
[proxy:0:0@login4] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file ABYSS-P (No such file or directory)

abyss bin directory is in my path. I see a file named ABYSS in the path but there is nothing called ABYSS-P (I used find . -name ABYSS-P and there is nothing)

openmpi is loaded as a module in the job script (although here I am not making an explicit mpi run)
is there a problem in the compilation step ? Can you please help me?

[Anthony Raymond]

Hi,

You likely didn't compile abyss with MPI support. You'll need to reconfigure and recompile ABySS. When running ./configure, you'll need to use the --with-mpi option. There's an example usage of this option in the Compiling ABySS from source section of the README:

https://github.com/bcgsc/abyss#compiling-abyss-from-source

When you run ./configure, you should see 'yes' at the ends of these four lines:

checking mpi.h usability... yes

checking mpi.h presence... yes

checking for mpi.h... yes

checking for MPI_Init in -lmpi... yes

Note: I've seen a couple people have similar compilation issues where they installed the libraries only for Open-MPI and not the MPI headers, which means you may need to install Open-MPI from source.

Then when you run `make install`, an ABYSS-P executable should be installed in the same path as the other ABySS executables.

Let me know how it goes,

Tony

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[Tevfik Hamdi Kitapci]

Hi Tony,

This is the command I used to configure

./configure --prefix=/home/tkitapci/software/abyss-1.5.2/INSTALL CPPFLAGS=-I/c1/modulefiles/sparsehash/ --with-mpi=/c1/apps/openmpi/

the folder /c1/apps/openmpi/ contains the following folders

1.8/ gcc/ intel/ Rmpi/

is this the correct way of doing it ? or should I be pointing to another folder or one of these subfolders. Is there a "test" method to see if I compiled abyss correctly with mpi ?

Thanks
Best Regards
Hamdi Kitapci

[Anthony Raymond]

Hi Hamdi,

The test here would be was the ABYSS-P executable generated. I usually use the linux command `which`. You won't see the path to your ABySS install if you run `which ABYSS-P`. Try `which ls` and `which abyss` to see what I mean.

Based on the folders you listed, I would say that you aren't specifying the path correctly. You should see a lib/ (or possibly lib64/) and include/ folder when you `ls` the folder given to the --with-mpi option.

Cheers,

Tony

[Tevfik Hamdi Kitapci]

Hi,

Thanks Anthony I found the folder with /lib and /bin and ABYSS-P is generated this time but I have multiple options

--with-mpi=/c1/apps/openmpi/1.8/gcc/4.7/cpu/
--with-mpi=/c1/apps/openmpi/gcc/64/1.7.4/
--with-mpi=/c1/apps/openmpi/gcc/64/1.8/
--with-mpi=/c1/apps/openmpi/intel/64/1.7.4

etc...

all of those folders generate ABYSS-P is abyss compatible with any version of openmpi?

Thanks
Best Regards
Hamdi Kitapci

[Anthony Raymond]

Hi Hamdi,

You'll want to use the same version of mpirun as the version you used to compile ABySS with. Other than that, any version of OpenMPI should work fine.

You can specify the exact mpirun command to use when you run abyss-pe like so:

abyss-pe mpirun=/c1/apps/openmpi/1.8/gcc/4.7/cpu/bin/mpirun …

Cheers,

Tony