problem installing ExaML

Andrés Parada

unread,

Jul 23, 2015, 8:00:57 AM7/23/15

to raxml

Dear raxml and examl users,

I got this error while trying to install examl typing cd ../examl/

make -f Makefile.SSE3.gcc

I just installed openmpi before this step.

andrelo@manya:~/OMA/ExaML-master/examl$ make -f Makefile.SSE3.gcc

mpicc -D_GNU_SOURCE -D__SIM_SSE3 -msse3 -fomit-frame-pointer -funroll-loops -D_OPTIMIZED_FUNCTIONS -D_USE_ALLREDUCE -O2 -c -o axml.o axml.c

mpicc: error while loading shared libraries: libopen-pal.so.6: cannot open shared object file: No such file or directory

make: *** [axml.o] Error 127

I put export PATH=$PATH:/home/andrelo/.openmpi/bin && export PATH=$PATH:/home/andrelo/.openmpi/lib in the ~/.profile -this has worked for other binaries-

Is there a way to fix this? Thanks in advance

Andrés

Alexey Kozlov

unread,

Jul 23, 2015, 8:15:02 AM7/23/15

to ra...@googlegroups.com

Dear Andrés,

this is MPI configuration problem, have you tried setting LD_LIBRARY_PATH to the directory where your openmpi libs were
installed?

See also:
http://www.open-mpi.org/faq/?category=running#run-prereqs

Best,
Alexey

On 23.07.2015 14:00, Andrés Parada wrote:
> Dear raxml and examl users,
>

> I got this error while trying to install examl typing /cd ../examl//
> /make -f Makefile.SSE3.gcc /

>
> I just installed openmpi before this step.
>

> /andrelo@manya:~/OMA/ExaML-master/examl$ make -f Makefile.SSE3.gcc /
> /mpicc -D_GNU_SOURCE -D__SIM_SSE3 -msse3 -fomit-frame-pointer -funroll-loops -D_OPTIMIZED_FUNCTIONS -D_USE_ALLREDUCE
> -O2 -c -o axml.o axml.c/
> /mpicc: error while loading shared libraries: libopen-pal.so.6: cannot open shared object file: No such file or directory/
> /make: *** [axml.o] Error 127/
> /
> /

> I put export PATH=$PATH:/home/andrelo/.openmpi/bin && export PATH=$PATH:/home/andrelo/.openmpi/lib in the ~/.profile
> -this has worked for other binaries-
>
> Is there a way to fix this? Thanks in advance
>
> Andrés
>

> --
> You received this message because you are subscribed to the Google Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.

Andrés Parada

unread,

Jul 23, 2015, 8:23:03 AM7/23/15

to ra...@googlegroups.com

OK, I didn't know what went wrong, I added the bin and lib folder to my .profile

I put them in that folder since I chose that folder since I installed it in /home/andrelo/.openmpi

export PATH=$PATH:/home/andrelo/.openmpi/bin

export PATH=$PATH:/home/andrelo/.openmpi/lib

Thanks

You received this message because you are subscribed to a topic in the Google Groups "raxml" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/raxml/ptc0wm1EuYE/unsubscribe.
To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.

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

--

Postdoctoral Associate

Instituto de Cs Ambientales y Evolutivas

Universidad Austral de Chile

Campus Isla Teja s/n

Valdivia, Chile

Alexey Kozlov

unread,

Jul 23, 2015, 8:26:47 AM7/23/15

to ra...@googlegroups.com

Yes, so now you need to add

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/andrelo/.openmpi/lib

as well, this should fix it.

Alexey

On 23.07.2015 14:22, Andrés Parada wrote:
> OK, I didn't know what went wrong, I added the bin and lib folder to my .profile
>
> I put them in that folder since I chose that folder since I installed it in /home/andrelo/.openmpi
>
> export PATH=$PATH:/home/andrelo/.openmpi/bin
> export PATH=$PATH:/home/andrelo/.openmpi/lib
>
> Thanks
>

> El jue., 23 de jul. de 2015 a la(s) 9:15 a. m., Alexey Kozlov <alexei...@gmail.com <mailto:alexei...@gmail.com>>

> raxml+un...@googlegroups.com <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml+un...@googlegroups.com <mailto:raxml%2Bunsu...@googlegroups.com>>.

> > For more options, visit https://groups.google.com/d/optout.
>
> --
> You received this message because you are subscribed to a topic in the Google Groups "raxml" group.
> To unsubscribe from this topic, visit https://groups.google.com/d/topic/raxml/ptc0wm1EuYE/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com

> <mailto:raxml%2Bunsu...@googlegroups.com>.

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

> Postdoctoral Associate
>
> Instituto de Cs Ambientales y Evolutivas
> Universidad Austral de Chile
> Campus Isla Teja s/n
> Valdivia, Chile
>

Alexander Todorov Tzanov

unread,

Dec 19, 2016, 11:26:22 AM12/19/16

to raxml

I am trying to install latest ExaML with gcc 4.4.7 and openmpi. Got error:

avxLikelihood.c: In function ‘newviewGTRGAMMAPROT_AVX_LG4’:

avxLikelihood.c:889: error: incompatible type for argument 2 of ‘_mm256_maskstore_pd’