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Running parallel charmm problem : libcxa.so.5
#5065 01/18/05 10:58 AM
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sarah Offline OP
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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

Re: Running parallel charmm problem : libcxa.so.5
sarah #5066 01/18/05 11:24 AM
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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.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Running parallel charmm problem -another problem!!
lennart #5067 01/18/05 01:09 PM
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sarah Offline OP
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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

Re: Running parallel charmm problem -another problem!!
sarah #5068 01/18/05 01:23 PM
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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,...).


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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