error: No network interfaces were found for out-of-band communications. We require at least one available network for out-of-band messaging.

Cameron Prybol

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Jul 1, 2016, 4:42:32 PM7/1/16

to Trans-ABySS

Hi,

I've received the error message in the subject-line and don't know what out-of-band communications are or where to start with fixing this issue. Full output of the run is below:

```

Trans-ABySS 1.5.4

CMD: /home/cjprybol/Software/transabyss-1.5.4/transabyss --pe /scratch/PI/euan/cameron/Projects/HCM-regulation/Data/merged_1.fq.gz /

scratch/PI/euan/cameron/Projects/HCM-regulation/Data/merged_2.fq.gz --outdir /scratch/PI/euan/cameron/Projects/HCM-regulation/Abyss

--threads 16

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

Found Trans-ABySS directory at: /home/cjprybol/Software/transabyss-1.5.4

Found Trans-ABySS `bin` directory at: /home/cjprybol/Software/transabyss-1.5.4/bin

Found script at: /home/cjprybol/Software/transabyss-1.5.4/bin/skip_psl_self.awk

Found script at: /home/cjprybol/Software/transabyss-1.5.4/bin/skip_psl_self_ss.awk

Found `blat' at /home/cjprybol/.linuxbrew/bin/blat

Found `MergeContigs' at /home/cjprybol/.linuxbrew/bin/MergeContigs

Found `abyss-filtergraph' at /home/cjprybol/.linuxbrew/bin/abyss-filtergraph

Found `abyss-map' at /home/cjprybol/.linuxbrew/bin/abyss-map

Found `abyss-pe' at /home/cjprybol/.linuxbrew/bin/abyss-pe

Found `abyss-junction' at /home/cjprybol/.linuxbrew/bin/abyss-junction

# CPU(s) available: 16

# thread(s) requested: 16

# thread(s) to use: 16

CMD: bash -euo pipefail -c 'abyss-pe --directory=/scratch/PI/euan/cameron/Projects/HCM-regulation/Abyss k=32 name=transabyss E=0 e=2

c=2 j=16 transabyss-1.fa transabyss-1.adj q=3 se="/scratch/PI/euan/cameron/Projects/HCM-regulation/Data/merged_1.fq.gz /scratch/PI/

euan/cameron/Projects/HCM-regulation/Data/merged_2.fq.gz"'

make: Entering directory `/scratch/PI/euan/cameron/Projects/HCM-regulation/Abyss'

/home/cjprybol/.linuxbrew/bin/mpirun -np 16 ABYSS-P -k32 -q3 -e2 -E0 -c2 --coverage-hist=coverage.hist -s transabyss-bubbles.fa

-o transabyss-1.fa /scratch/PI/euan/cameron/Projects/HCM-regulation/Data/merged_1.fq.gz /scratch/PI/euan/cameron/Projects/HCM-regul

ation/Data/merged_2.fq.gz

[sh-17-9.local:88517] [[36120,0],0] ORTE_ERROR_LOG: Address family not supported by protocol in file oob_tcp_listener.c at line 120

[sh-17-9.local:88517] [[36120,0],0] ORTE_ERROR_LOG: Address family not supported by protocol in file oob_tcp_component.c at line 639

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

No network interfaces were found for out-of-band communications. We require

at least one available network for out-of-band messaging.

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

[sh-17-9.local:88517] [[36120,0],0] ORTE_ERROR_LOG: Not initialized in file util/session_dir.c at line 579

make: *** [transabyss-1.fa] Error 213

make: Leaving directory `/scratch/PI/euan/cameron/Projects/HCM-regulation/Abyss'

ERROR: CMD ended with status code 2

```

The cluster I am trying to run this on uses a Slurm job scheduler. I'm not sure if that has anything to do with the problem. I receive the same error message when running the job interactively or when submitting a job to the job scheduler to be run non-interactively. I also receive the same error when running single-core without the threads option.

The system I am working on has openmpi/1.10.2 installed, which I tried loading but that had no effect. I also googled "out-of-band slurm", which returned lots of results, but nothing that gave me any leads.

Any ideas?

Thanks!

Cameron

Ka Ming Nip

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Jul 1, 2016, 7:46:09 PM7/1/16

to trans...@googlegroups.com

Hi Cameron,

Do you get this error immediately? or was it after a while? I actually have never heard of this error before.
Were you able to assemble our tiny sample data set?

Thanks,
Ka Ming

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Cameron Prybol [cameron...@gmail.com]
Sent: July 1, 2016 1:42 PM
To: Trans-ABySS
Subject: error: No network interfaces were found for out-of-band communications. We require at least one available network for out-of-band messaging.

--
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Cameron Prybol

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Jul 2, 2016, 6:53:57 PM7/2/16

to trans...@googlegroups.com

Hi Ka,

I was not able to assemble the sample data by running `./assemble.sh` in the directory `transabyss-1.5.4/sample_dataset/`, it returns the same error.

I tracked the problem down to being MPI by finding similar error messages and feedback here -> https://www.open-mpi.org/community/lists/users/2014/10/25473.php

Their suggested fix was to check ipv6, and I reinstalled openmpi on linuxbrew to check what the configuration options are.

```

./configure --prefix=/home/cjprybol/.linuxbrew/Cellar/open-mpi/1.10.2 --disable-silent-rules --enable-ipv6 --with-libevent=/home/cjprybol/.linuxbrew/opt/libevent --with-sge

```

As you can see, the ipv6 flag is there, so I guess that's not the issue. Not sure what may or may not be the problem with the other flags.

Because of that linuxbrew openmpi problem, I removed my abyss install from linuxbrew and tried to reinstall it using the openmpi library that was installed by the staff who manage the cluster.

Now I've bypassed the openmpi problem, but now I'm having problems with ABYSS-P. I'm not sure if now I should move over to an Abyss-specific help area, but if so, let me know.

Here are the several ways that I've tried to install abyss, and the errors associated with each. Now, either ABYSS-P cannot be found, or when ABYSS-P can be found, it is unable to find `libibverbs.so.1`. For the github installs, I also ran the procedure but did a `git checkout 1.5.2` to get the version specified in the readme for transabyss, and got the same output, so I've not included those attempts.

I'm happy to try and debug whichever error seems easiest to deal with. Googling the libibverbs.so.1 didn't return anything helpful, which was the error I tried to debug first.

The first line is the method for installation, and the rest of the code blocks are the truncated error messages / transabyss output with the relevant info.

```

brew install --ignore-dependencies abyss

CMD: bash -euo pipefail -c 'abyss-pe --directory=/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz"'

make: Entering directory `/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25'

/share/sw/free/openmpi/1.10.2/gcc/4.8/bin/mpirun -np 1 ABYSS-P -k25 -q3 -e1 -E0 -c1 --coverage-hist=coverage.hist -s test.k25-bubbles.fa -o test.k25-1.fa /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz

ABYSS-P: error while loading shared libraries: libibverbs.so.1: cannot open shared object file: No such file or directory

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

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

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

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

mpirun detected that one or more processes exited with non-zero status, thus causing

the job to be terminated. The first process to do so was:

Process name: [[44272,1],0]

Exit code: 127

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

```

brew install --build-from-source --ignore-dependencies abyss

CMD: bash -euo pipefail -c 'abyss-pe --directory=/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz"'

make: Entering directory `/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25'

/share/sw/free/openmpi/1.10.2/gcc/4.8/bin/mpirun -np 1 ABYSS-P -k25 -q3 -e1 -E0 -c1 --coverage-hist=coverage.hist -s test.k25-bubbles.fa -o test.k25-1.fa /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz

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

mpirun was unable to find the specified executable file, and therefore

did not launch the job. This error was first reported for process

rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command

line parameter option (remember that mpirun interprets the first

unrecognized command line token as the executable).

Node: sh-17-9

Executable: ABYSS-P

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

```

git clone https://github.com/bcgsc/abyss.git

cd abyss

./autogen.sh

./configure \

--prefix=/share/PI/euan/cameron

make && make install

CMD: bash -euo pipefail -c 'abyss-pe --directory=/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz"'

make: Entering directory `/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25'

/share/sw/free/openmpi/1.10.2/gcc/4.8/bin/mpirun -np 1 ABYSS-P -k25 -q3 -e1 -E0 -c1 --coverage-hist=coverage.hist -s test.k25-bubbles.fa -o test.k25-1.fa /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz

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

mpirun was unable to find the specified executable file, and therefore

did not launch the job. This error was first reported for process

rank 0; it may have occurred for other processes as well.

NOTE: A common cause for this error is misspelling a mpirun command

line parameter option (remember that mpirun interprets the first

unrecognized command line token as the executable).

Node: sh-17-9

Executable: ABYSS-P

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

```

git clone https://github.com/bcgsc/abyss.git

cd abyss

./autogen.sh

./configure \

--prefix=/share/PI/euan/cameron \

--with-boost=/home/cjprybol/.linuxbrew/Cellar/boost/1.60.0_2/include \

--with-mpi=/share/sw/free/openmpi/1.10.2/gcc/4.8

make && make install

CMD: bash -euo pipefail -c 'abyss-pe --directory=/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25 k=25 name=test.k25 E=0 e=1 c=1 j=2 test.k25-1.fa test.k25-1.adj q=3 se="/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz"'

make: Entering directory `/share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/test.k25'

/share/sw/free/openmpi/1.10.2/gcc/4.8/bin/mpirun -np 1 ABYSS-P -k25 -q3 -e1 -E0 -c1 --coverage-hist=coverage.hist -s test.k25-bubbles.fa -o test.k25-1.fa /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_1.fq.gz /share/PI/euan/cameron/transabyss-1.5.4/sample_dataset/reads/rnaseq_2.fq.gz

ABYSS-P: error while loading shared libraries: libibverbs.so.1: cannot open shared object file: No such file or directory

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

Primary job terminated normally, but 1 process returned

a non-zero exit code.. Per user-direction, the job has been aborted.

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

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

mpirun detected that one or more processes exited with non-zero status, thus causing

the job to be terminated. The first process to do so was:

Process name: [[3147,1],0]

Exit code: 127

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

```

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Ka Ming Nip

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Jul 2, 2016, 10:36:47 PM7/2/16

to trans...@googlegroups.com

Hi Cameron,

This is indeed an issue with your ABySS installation. Best to get help from abyss...@googlegroups.com. Sorry, I wasn't of much help to you.

Just so you know, the current version of Trans-ABySS only works with ABySS version 1.5.2.

Ka Ming

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Cameron Prybol [cameron...@gmail.com]

Sent: July 2, 2016 3:53 PM
To: trans...@googlegroups.com
Subject: Re: error: No network interfaces were found for out-of-band communications. We require at least one available network for out-of-band messaging.

On Fri, Jul 1, 2016 at 4:41 PM, Ka Ming Nip <km...@bcgsc.ca<mailto:km...@bcgsc.ca>> wrote:
Hi Cameron,

Do you get this error immediately? or was it after a while? I actually have never heard of this error before.
Were you able to assemble our tiny sample data set?

Thanks,
Ka Ming

--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________

From: trans...@googlegroups.com<mailto:trans...@googlegroups.com> [trans...@googlegroups.com<mailto:trans...@googlegroups.com>] On Behalf Of Cameron Prybol [cameron...@gmail.com<mailto:cameron...@gmail.com>]

To unsubscribe from this group and stop receiving emails from it, send an email to trans-abyss...@googlegroups.com<mailto:trans-abyss%2Bunsu...@googlegroups.com><mailto:trans-abyss...@googlegroups.com<mailto:trans-abyss%2Bunsu...@googlegroups.com>>.

For more options, visit https://groups.google.com/d/optout.

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