CHARMM Development Project Forums User Discussion & Questions Installation and Testing Running parallel charmm problem : libcxa.so.5

I compiled the parallel version of charmm and attempted to run it with the following command :charmm -p4wd . -p4pg file < minimise2 > out

where file is :
host61 0
host61 1 ~/CHARMM_exec/charmm
host62 1 ~/CHARMM_exec/charmm
host62 1 ~/CHARMM_exec/charmm
host63 1 ~/CHARMM_exec/charmm
host63 1 ~/CHARMM_exec/charmm

But I always get the following error : error while loading shared libraries: libcxa.so.5: cannot open shared object file: No such file or directory.

How can I correct this error. I would be very grateful of help

Sarah

ifort is probably not installed, or not installed in the same place as on the machine used to install charmm, on one or more of the execution nodes.
Add -static to the appropriate LD definition in Makefile_gnu and run install.com again.

Hi, thanks for that. I have another problem now in the creation of the nodelist (I think !).

In the documentation, there is the following :

host1 0
host2 1 ~charmm/exec/gnu/charmm
host3 1 ~charmm/exec/gnu/charmm

I have interpreted as it meaning the following :
host61 0
host61 1 ~charmm/exec/gnu/charmm
host62 1 ~charmm/exec/gnu/charmm
etc

where 61, 62 are the name of the nodes. However, when I use the following command line ~charmm/exec/gnu/charmm -p4wd . -p4pg file < input >out

I get the following error :
p0_27637: (60.362311) entry 0: host61 0 0
p0_27637: (60.362327) entry 1: host61 1 1 ~/c30b2/exec/gnu/charmm sarah
p0_27637: (60.362337) entry 2: host62 1 2 ~/c30b2/exec/gnu/charmm sarah
p0_27637: (60.362347) entry 3: host62 1 3 ~/c30b2/exec/gnu/charmm sarah
p0_27637: (60.362357) entry 4: host63 1 4 ~/c30b2/exec/gnu/charmm sarah
p0_27637: (60.362367) entry 5: host63 1 5 ~/c30b2/exec/gnu/charmm sarah
p0_27637: p4_error: Could not gethostbyname for host host61; may be invalid name
: 61

What does this mean ?

Many thanks

Sarah

host1 is supposed to be replaced by the name of the first machine, etc.
so assuming that your machines have names red, blue, and green a hostfile like this should work (for one charmm process on each machine, and red is the machine on which you start the job):
red 0 ~charmm/exec/gnu/charmm
blue 1 ~charmm/exec/gnu/charmm
green 1 ~charmm/exec/gnu/charmm

if you want two processes/machine your mpich installation has to be configured for shared-memory communication, and you increase the process counts by one in the example above. note that certain modules in charmm require that the number of CPUs in a parallel job is a power of two (1,2,4,8,...).