Errors encountered while running MEME

[Zoran Lee]

I wanted to reach out and inquire if anyone else has encountered the same issue as I have while running MEME on a remote server.

Due to my technical proficiency, I installed MEME from conda.

First, I am unable to execute MEME without the "mpirun" command. Despite following the standard steps for MEME installation and configuration, the program does not seem to run properly without the presence of "mpirun". I encountered the following error:

$ meme
--------------------------------------------------------------------------
As of version 3.0.0, the "sm" BTL is no longer available in Open MPI.

Efficient, high-speed same-node shared memory communication support in
Open MPI is available in the "vader" BTL.  To use the vader BTL, you
can re-run your job with:

    mpirun --mca btl vader,self,... your_mpi_application
--------------------------------------------------------------------------
--------------------------------------------------------------------------
A requested component was not found, or was unable to be opened.  This
means that this component is either not installed or is unable to be
used on your system (e.g., sometimes this means that shared libraries
that the component requires are unable to be found/loaded).  Note that
Open MPI stopped checking at the first component that it did not find.

Host:      cngb-xcompute-0-10.cngb.sz.hpc
Framework: btl
Component: sm
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems.  This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  mca_bml_base_open() failed
  --> Returned "Not found" (-13) instead of "Success" (0)
--------------------------------------------------------------------------
[cngb-xcompute-0-10:06383] *** An error occurred in MPI_Init
[cngb-xcompute-0-10:06383] *** reported by process [537001985,0]
[cngb-xcompute-0-10:06383] *** on a NULL communicator
[cngb-xcompute-0-10:06383] *** Unknown error
[cngb-xcompute-0-10:06383] *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
[cngb-xcompute-0-10:06383] ***    and potentially your MPI job)

I have encountered another issue as well. When I use 'mpirun' to run MEME, it consistently throws an error and occasionally fails to generate the HTML files correctly. 

My running command is as follows:

$ mpirun -np 1 --use-hwthread-cpus --mca btl vader,self meme BX_1000bp_100bp_ab.fasta -dna -oc BX_1000bp_100bp_ab_result -nostatus -time 14400 -mod zoops -nmotifs 10 -minw 50 -maxw 60 -objfun classic -revcomp -markov_order 0

The error message is as follows:

--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 0 on
node cngb-compute-f21-4 exiting improperly. There are three reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

3. this process called "MPI_Abort" or "orte_abort" and the mca parameter
orte_create_session_dirs is set to false. In this case, the run-time cannot
detect that the abort call was an abnormal termination. Hence, the only
error message you will receive is this one.

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

You can avoid this message by specifying -quiet on the mpirun command line.
--------------------------------------------------------------------------

Thank you all for your time and collaboration. I'm looking forward to any feedback you may have.

[Zoran Lee]

Hello everyone, I've made some progress in resolving the issue. I found a command "meme_xml_to_html" in the bin directory of MEME, which allows quick conversion of XML files to HTML. I hope this can be helpful to others.

[cegrant]

Hi Zoran,

We have no connection to the conda MEME Suite package so we can't help you with that. Based on the error messages your are getting it looks like it is using a very dated version of the MEME Suite. MEME no longer requires explicitly using mpirun. MEME will automatically call mpirun internally. See the description of the '-p' option in the MEME documentation. The official source code for the MEME Suite can be found here, and the installation guide here.

Charles