new installation liggghts make fedors problem

Submitted by jeen1 on Sun, 09/18/2011 - 03:10

Hi, I tred to install liggghts for the first time. (new to Linux as well).

After typing 'make fedora' in /src got a whole bunches of can't find files. I looked into the src directory, and they are all there.

make[1]: *** [memory.d]Error 1

memory.cpp:14:17: fatal error: mpi.h: No such file or directory
compilation terminated.then it leaves the directory
make[1] Leaving director ' /home/.../liggghts_1p4p3/src/Obj_fedora'
make: ***[fedors] Error 2.

Not sure how to proceed from here. Any help is appreciated

Forums:

prasantud | Sun, 09/18/2011 - 07:15

Hi Jeen,
you need to compile serial version initially. so type make serial
For parallel you need to install open-mpi.
I had similar problems initially, keep on posting them.
Samantaray

jeen1 | Sun, 09/18/2011 - 17:37

Yes, make serial did work. What did you do next?

I have mpi installed. However, when I check " which mpirun"

I got "/usr/lib64/mpich2/bin/mpirun" not "/usr/lib64/openmpi/bin/mpirun". I have mpich2, not openmpi as stated on the instruction. Not sure if this is the problem. (But mpirun and mpic++ commands both run.)

When I did make fedora again, it complains not finding mpi.h and terminate with error.

Any suggestion. Not sure if I should try redo mpi install. Thanks.

ckloss's picture

ckloss | Sun, 09/18/2011 - 18:06

>>But mpirun and mpic++ commands both run
If you compile with mpic++, not finding mpi.h should not occur...

I would try to either re-install openmpi or to create symbolic links with "ln -s"

Christoph

jeen1 | Mon, 09/19/2011 - 06:28

I reinstall fedora, and follow each of the step include git and all to install flagghts. Then I "make fedora" and at the end, received the message:
text data bss dec hex filename
2640167 104184 1248 2745599 29e4ff ../lmp_fedora
make[1]: Leaving directory `/.../cfdem/myliggghts/src/Obj_fedora'

After link symbol to liggghts, I typed liggghts on command, here I got an error,
liggghts: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory
I have both openmpi and openmpi-devel installed as per instruction. Not sure what happened?
I have also link symbol, "sudo ln -s /usr/lib64/openmpi/lib/libmpi_cxx.so.1 /usr/lib"

Any suggestion?

Much appreciated.

ckloss's picture

ckloss | Mon, 09/19/2011 - 09:25

this is a bug in the openmpi installation in fedora, you have to manually set the symbolic links for libmpi_cxx.so.1 as well as for all other libs that are missing (you will get similar errors)

Christoph

jeen1 | Mon, 09/19/2011 - 17:26

While it gave me the error of not linking with libmpi_cxx_so_1, I checked and it was already there in usr/lib, but after I also put in a symbol link for libmpi_so_1, then it works.

My summary of resolving the problem of using Fedora is as follows, do

sudo ln -s libmpi_cxx_so_0 usr/lib
sudo ln -s libmpi_cxx_so_1 usr/lib
sudo ln -s libmpi_so_1 usr/lib

Thanks for all the help!