AMBER Archive (2005)

Subject: AMBER: error in parallel

From: gsmith_at_ibab.ac.in
Date: Mon Jan 10 2005 - 02:18:51 CST

dear users,

Iam running a simulation of a biomolecule containing ~60,000 atoms.I
sucessfully completed 2.2ns of simulation on cluster with 4 nodes on linux
platform (intel pentium,rethatlinux 7.3).then i tried to continue the job
on a cluster with 4 nodes with dual processors (intel xeon; red hat 7.2)

I used sander to run the simulation but hte job doesnot seem to produce
any output,neither it does not run.it gives the following error

p0_26741: (1000.390736) entry 9: ~ 1 /home/programs/amber6/exe/sander
gsmith
p0_26741: (1000.390753) entry 10: master 1
/home/gsmith/amber6/exe/sander gs mith
p0_26741: (1000.390771) entry 11: node1 1
/home/gsmith/amber6/exe/sander gsm ith
p0_26741: (1000.390788) entry 12: node2 1
/home/gsmith/amber6/exe/sander gsm ith
p0_26741: (1000.390805) entry 13: node3 1
/home/gsmith/amber6/exe/sander gsm ith
p0_26741: (1000.390822) entry 14: ~ 1 /home/programs/amber6/exe/sander
gsmith
p0_26741: (1000.390838) entry 15: master 1
/home/gsmith/amber6/exe/sander programs
p0_26741: p4_error: Could not gethostbyname for host ~; may be invalid name
: 1001

*But when i try to run a job with ~15,000 atoms ,the job runs succesfully.
I have about 5GB free space in master node and about 2gb in slave nodes.is
the space problem?

*has anyone come across such problem.any help or suggestion regarding this
is welcome.thanking in advance.

-smith

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