Dear Edo,
The ldd now is
[user@localhost LINUX64]$ l
total 77916
drwxrwxr-x. 2 user user 4096 Nov 9 23:40 .
drwxrwxr-x. 3 user user 4096 Oct 12 19:10 ..
-rwxrwxr-x. 1 user user 20548 Nov 9 22:40 depend.x
-rwxrwxr-x. 1 user user 79750571 Nov 9 23:40 nwchem
[user@localhost LINUX64]$ ldd ./nwchem
linux-vdso.so.1 => (0x00007fff2f5ff000)
libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x0000003cae200000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003a17800000)
libutil.so.1 => /lib64/libutil.so.1 (0x0000003a28800000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003a17400000)
libm.so.6 => /lib64/libm.so.6 (0x0000003a17c00000)
libc.so.6 => /lib64/libc.so.6 (0x0000003a17000000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003a1dc00000)
/lib64/ld-linux-x86-64.so.2 (0x0000003a16c00000)
The result of running nwchem on dna still fails.
[user@localhost LINUX64]$ cd ../../examples/md/dna
[user@localhost dna]$ rm ./*
rm: cannot remove `./temp': Is a directory
[user@localhost dna]$ rm .header
[user@localhost dna]$ cp temp/* .
[user@localhost dna]$ l
total 44
drwxr-x---. 3 user user 4096 Nov 9 23:50 .
drwxr-x---. 23 user user 4096 Oct 31 15:19 ..
-rw-r-----. 1 user user 420 Nov 9 23:50 dna.nw
-rw-r-----. 1 user user 28631 Nov 9 23:50 dna.pdb
drwxrwxr-x. 2 user user 4096 Nov 1 16:17 temp
Job information
---------------
hostname = localhost.localdomain
program = /opt/nwchem_intel2013_openmpi16/bin/nwchem
date = Fri Nov 9 23:51:08 2012
compiled = Fri_Nov_09_22:46:51_2012
source = /home/user/Documents/codes/nwchem-6.1.1-src
nwchem branch = 6.1.1
input = dna.nw
prefix = dna.
data base = ./dna.db
status = startup
nproc = 1
time left = -1s
Memory information
------------------
heap = 131072001 doubles = 1000.0 Mbytes
stack = 131072001 doubles = 1000.0 Mbytes
global = 262144000 doubles = 2000.0 Mbytes (distinct from heap & stack)
total = 524288002 doubles = 4000.0 Mbytes
verify = yes
hardfail = no
...
Force field amber
Directories used for fragment and segment files
/opt/nwchem_intel2013_openmpi16/data/amber_s/
/opt/nwchem_intel2013_openmpi16/data/amber_q/
/opt/nwchem_intel2013_openmpi16/data/amber_x/
/opt/nwchem_intel2013_openmpi16/data/amber_u/
./
Parameter files used to resolve force field parameters
/opt/nwchem_intel2013_openmpi16/data/amber_s/amber.par
/opt/nwchem_intel2013_openmpi16/data/amber_q/amber.par
/opt/nwchem_intel2013_openmpi16/data/amber_x/amber.par
/opt/nwchem_intel2013_openmpi16/data/amber_u/amber.par
./amber.par
PDB geometry dna.pdb
Created segment ./DT_5.sgm
Created segment ./DG.sgm
Created segment ./DC.sgm
Created segment ./DA_3.sgm
Created sequence ./dna.seq
Parameter file /opt/nwchem_intel2013_openmpi16/data/amber_s/amber.par
Parameter file /opt/nwchem_intel2013_openmpi16/data/amber_q/amber.par
Parameter file /opt/nwchem_intel2013_openmpi16/data/amber_x/amber.par
Parameter file /opt/nwchem_intel2013_openmpi16/data/amber_u/amber.par
Total charge 0.000000
Created topology dna.top
Topology dna.top
No command file found: Default restart directives
Solute centered in x-dimension
Solute centered in y-dimension
Solute centered in z-dimension
Boxsize determined to 1.968800 2.003300 2.599200
Created restart dna_em.rst
Reference coordinates read from dna_em.qrs
Number of atoms is 388
Topology read from dna.top
Opening trj file dna_md.trj
Closing trj file
Trajectory file header from dna_md.trj
Opening trj file dna_md.trj
Opening copy file dna_super.trj
0:Segmentation Violation error, status=: 11
(rank:0 hostname:localhost.localdomain pid:25539):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 0:: Inappropriate ioctl for device
0: ARMCI aborting 11 (0xb).
0: ARMCI aborting 11 (0xb).
system error message: Inappropriate ioctl for device
I am wondering is there a way to cleanly put the commands into my scripts?
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