Trouble with MEME & make test

[R. Blues]

Hello everyone,

I have already taken a look at earlier posts, but I have not been able to solve this :/

I have downloaded the most recent version of MEME, and installed it using the recommended parameters. However, I am unable to run the meme script (all their tests fail during the make test, with a SIGSEGV error). If I try to run the command meme, I get the following result:


*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x44000098
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7fca0ecef340]
[ 1] /usr/lib/libmpi.so.1(PMPI_Comm_rank+0x4b) [0x7fca0ef6763b]
[ 2] meme() [0x4221f3]
[ 3] meme() [0x403527]
[ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7fca0e93bec5]
[ 5] meme() [0x404f15]
*** End of error message ***


What should I do/try?

Here you can find the config.log, make.log, and also make_test and install logs (I have seen that in other cases, you ask for them, so... I attach them, just in case they can be of use :) )

Thank you very much; I really need to make it work for my paper!

[CharlesEGrant]

It looks like you have a problem with your MPI setup. Try turning off support for parallel processing. To do that, run

./configure [other options] --enable-serial

make clean

make

make test

[R. Blues]

Yes, it worked! Thank you very much!

Just out of curiosity, but... where does it indicate the problem with my MPI setup?

Do you know of any way to fix it, so I can use the parallel version?

Thank you very much.

[CharlesEGrant]

Hi R,

I knew it was something to do with your MPI setup because of the stack trace in the error message you provided:

Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x44000098
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7fca0ecef340]
[ 1] /usr/lib/libmpi.so.1(PMPI_Comm_rank+0x4b) [0x7fca0ef6763b]
[ 2] meme() [0x4221f3]

Note that the 2nd item from the top of the stack is a call into /usr/lib/libmpi.so. I recognized that as the MPI library.

Unfortunately helping you with the MPI installation is beyond the scope of help we can offer. You may need to find a local system administrator to help you with that. My guess is that you may have multiple copies of MPI installed in different locations. The call stack indicates that it's trying to use a copy of the MPI library in /usr/lib, but all the MPI references in your config.log file seem to refer to a copy of MPI in /home/r/anaconda:

MPICC='/home/r/anaconda/bin/mpicc'

MPIFLAGS='-DPARALLEL '

MPIINC='-DMPI -I/home/r/anaconda/include'

MPILIBDIR='/home/r/anaconda/lib'

MPIRUN='/home/r/anaconda/bin/mpirun'

MPITYPE='mpich'

MPI_CMD='/home/r/anaconda/bin/mpirun -np'

I'd try getting a simple MPI program to work, and then go back to retry building the MEME Suite with MPI support turned on.

[R. Blues]

Hi Charles,

Thank you very much. It was really useful, and I also have learnt a little about error tracing.

About the MPI, knowing that, I have just solved the problem, so... Finally I can use Meme at its fullest! :) It was taking indeed a lot of time with a single thread, I hope I can accelerate it now.

Have a nice day!