Question: Problems Installing Meme
gravatar for Qmarqeva
10.2 years ago by
Qmarqeva20 wrote:


These days a was trying to install the MEME version 4.4.0 over a cluster that is running ROCKS 5.2 (Chimichanga). But now i have some problems, because i like to use MPICH2, i had tried it for separately and it's ok but when i try to integrated with MEME the package don't install. I use this option of configuration:

./configure --enable-build-libxml2 --enable-build-libxslt --enable-openmp --with-mpidir=/opt/mpich2/gnu

but when i execute MAKE command some error happends:

libtool: link: /opt/mpich2/gnu/bin/mpicc -I.. -DPARALLEL -I../../src/libxml2/include -I../../src/ -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -O3 -o meme_p meme_p-banner.o meme_p-branching_search.o meme_p-calculate_p_y.o meme_p-discretize.o meme_p-display.o meme_p-dpalign.o meme_p-em.o meme_p-init.o meme_p-justlike.o meme_p-likelihood.o meme_p-llr.o meme_p-logs.o meme_p-meme.o meme_p-meme-print-html.o meme_p-meme_util.o meme_p-message.o meme_p-mp.o meme_p-oops.o meme_p-partition.o meme_p-prior.o meme_p-psp.o meme_p-pssm-distr.o meme_p-read_seq_file.o meme_p-regress.o meme_p-seed.o meme_p-seed_diffs.o meme_p-seq2theta.o meme_p-sp_matrix.o meme_p-starts.o meme_p-subseq7.o meme_p-tcm.o meme_p-verbosity.o  ../.libs/libcommon.a ../../src/libxml2/.libs/libxml2.a ../../src/libxslt/.libs/libxslt.a -lm
meme_p-message.o: In function `reduce_across_s_points':
message.c:(.text+0x355): undefined reference to `ompi_mpi_comm_world'
message.c:(.text+0x420): undefined reference to `ompi_mpi_double'
meme_p-message.o: In function `reduce_across_models':
message.c:(.text+0x919): undefined reference to `ompi_mpi_comm_world'
message.c:(.text+0xc35): undefined reference to `ompi_mpi_double'
meme_p-mp.o: In function `mpBroadcast':
mp.c:(.text+0xd): undefined reference to `ompi_mpi_comm_world'
mp.c:(.text+0x15): undefined reference to `ompi_mpi_byte'
meme_p-mp.o: In function `mpReduceAdd':
mp.c:(.text+0x56): undefined reference to `ompi_mpi_comm_world'
mp.c:(.text+0x5e): undefined reference to `ompi_mpi_op_sum'
mp.c:(.text+0x69): undefined reference to `ompi_mpi_int'
meme_p-mp.o: In function `mpMyID':
mp.c:(.text+0x9a): undefined reference to `ompi_mpi_comm_world'
meme_p-mp.o: In function `mpNodes':
mp.c:(.text+0xcb): undefined reference to `ompi_mpi_comm_world'
meme_p-sp_matrix.o: In function `reduce_across_heaps':
sp_matrix.c:(.text+0x3f7): undefined reference to `ompi_mpi_comm_world'
sp_matrix.c:(.text+0x4ae): undefined reference to `ompi_mpi_double'
sp_matrix.c:(.text+0x4b5): undefined reference to `ompi_mpi_int'
sp_matrix.c:(.text+0x4bc): undefined reference to `ompi_mpi_int'
sp_matrix.c:(.text+0x4c3): undefined reference to `ompi_mpi_char'
collect2: ld returned 1 exit status
make[4]: *** [meme_p] Error 1
make[4]: Leaving directory `/home/usuario1/meme_4.4.0/src/parallel'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/usuario1/meme_4.4.0/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/usuario1/meme_4.4.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/usuario1/meme_4.4.0'
make: *** [all] Error 2

Please could you help me to solve this ??. Thanks for your response and sorry for write you but i'm so desesperate.

meme • 5.0k views
ADD COMMENTlink modified 10.2 years ago by Paulo Nuin3.7k • written 10.2 years ago by Qmarqeva20

This may be a related question: Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster

ADD REPLYlink modified 16 months ago by _r_am32k • written 10.2 years ago by Istvan Albert ♦♦ 86k
gravatar for Paulo Nuin
10.2 years ago by
Paulo Nuin3.7k
Paulo Nuin3.7k wrote:

First, OpenMP is one thing and MPI is another, completely different. I would try not using OpenMP if your compiler doesn't support it (I don't know which one comes with Rocks). So, remove the -enable-openmp from the configuration, make clean and try making again.

OpenMP is just an API that relies on C/C++ pragmas for parallelization on shared memory systems only, while MPI is an API that works on distributed memory systems. If you are running Rocks, chances are you are in a Beowulf system and MPI would be your best bet.

Another thing, is that I don't know if MEME needs both, but I don't think so.

EDIT: looking at your question again, check your MPIDIR that you are passing, it might be wrong or you're passing a wrong subdir to the configuration

ADD COMMENTlink modified 10.2 years ago • written 10.2 years ago by Paulo Nuin3.7k

This is correct: OpenMP is for multi-threading (one machine), MPI for clusters (multiple machines). For a ROCKS cluster, use MPI.

ADD REPLYlink written 10.2 years ago by Neilfws49k

Thanks for the help Paulo, you're right, i had was so confused about OpenMP and MPI... sorry... now i reconfigured without the option --enable-openmp and all is OK... and the MPIDIR is ok too.

I run the parallel test using runcheck_p script and nodes work fine, but i like to test some example using le command meme_p. Do you know one example?

Thanks for your time i appreciate it...

ADD REPLYlink modified 17 months ago by _r_am32k • written 10.2 years ago by Qmarqeva20

Sorry, but it has been quite sometime since I did anything on motif finding. I will put on my list of things to check and I comment here if I find anything useful for you.

ADD REPLYlink written 10.2 years ago by Paulo Nuin3.7k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1156 users visited in the last hour