From NWChem
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Posts 11
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| 5:18:04 AM PST - Thu, Dec 11th 2014 |
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Hello, all.
I'm compiling NWChem in an intel machine using ics(intel cluster studio) package.
The compile was successful, yet an error message halts the calculation.
It is the same situation either running in parallel or in background directly.
Here's my output.
Command: /home/kmh603/programs/nwchem-6.1/bin/LINUX64/nwchem simple.nw
Result:
argument 1 = simple.nw
======================== echo of input deck ========================
start simple
echo
geometry noautosym units angstrom
O -0.702196054 -0.056060256 0.009942262
H -1.022193224 0.846775782 -0.011488714
H 0.257521062 0.042121496 0.005218999
O 2.220871067 0.026716792 0.000620476
H 2.597492682 -0.411663274 0.766744858
H 2.593135384 -0.449496183 -0.744782026
end
memory 1000 mb
charge 0
BASIS SPHERICAL
O library aug-cc-pvqz
H library aug-cc-pvqz
end
DFT
XC XPBE96 CPBE96
END
TASK DFT energy
====================================================================
could not open a file in scratch directory:
------------------------------------------------------------------------
Fatal Error: scratch directory not accessible 911
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
0: TASK DFT energy
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error in the input file
------------------------------------------------------------------------
For more information see the NWChem manual at
http://www.nwchem-sw.org/index.php/NWChem_Documentation
For further details see manual section:
0:0:Fatal Error: scratch directory not accessible:: 911
(rank:0 hostname:jarvis pid:32486):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/armci.c:ARMCI_Error():208 cond:0
Last System Error Message from Task 0:: No such file or directory
application called MPI_Abort(comm=0x84000001, 911) - process 0
Same error occurs if I set SCRATCH_DIR in the input file like this:
could not open a file in scratch directory: /home/kmh603/nwchem
Also it fails if I use the command:
mpirun -np (either 1 or whatever number) /home/kmh603/programs/nwchem-6.1/bin/LINUX64/nwchem simple.nw
I'm not sure why it fails to find only scratch directory.
I think it should be a problem due to compile not permission because it was faild even in my own directory.
Setup for compile environment is as below:
setenv NWCHEM_TOP /home/kmh603/programs/nwchem-6.1
setenv NWCHEM_TARGET LINUX64
setenv ARMCI_NETWORK MPI-TS
setenv USE_MPI y
setenv USE_MPIF y
setenv USE_MPIF4 y
setenv MPI_LOC ${I_MPI_ROOT}
setenv MPI_LIB $MPI_LOC/lib64
setenv MPI_INCLUDE $MPI_LOC/include64
setenv LIBMPI "-lmpigf -lmpigi -lmpi_ilp64 -lmpi"
setenv NWCHEM_MODULES "qm"
setenv CC 'mpicc -cc=icc'
setenv FC 'mpif90 -f90=ifort'
setenv BLASOPT "-L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -liomp5"
and
$I_MPI_ROOT="/appl/intel/impi/4.0.3.008"
$MKLROOT="/appl/intel/composer_xe_2011_sp1.6.233/mkl"
mpif90="/appl/intel/impi/4.0.3.008/intel64/bin/mpif90"
I'm a novice at compiling, so any question or advice on my compiling setup will be helpful for me.
Thanks in advance.
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Edited On 5:42:44 AM PST - Thu, Dec 11th 2014 by Kmh603
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 9
Posts 1451
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| 9:42:55 PM PST - Tue, Dec 16th 2014 |
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What is the output of the commands
ls -l simple*
df .
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Edited On 9:43:11 PM PST - Tue, Dec 16th 2014 by Edoapra
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Clicked A Few Times
Threads 5
Posts 11
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| 10:38:33 PM PST - Tue, Dec 16th 2014 |
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Here are the outputs of the commands.
ls -l
-rw-r--r-- 1 kmh603 users 994 Dec 11 21:01 simple.cs
-rw-r--r-- 1 kmh603 users 504 Dec 11 21:07 simple.nw
-rw-rw-r-- 1 kmh603 users 5814 Dec 11 21:01 simple.out
df .
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sdb1 14418129792 916313312 12769417276 7% /home
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Edited On 10:39:02 PM PST - Tue, Dec 16th 2014 by Kmh603
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Edoapra Forum:Admin, Forum:Mod, bureaucrat, sysop
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Forum Vet
Threads 9
Posts 1451
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Clicked A Few Times
Threads 5
Posts 11
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| 6:43:06 PM PST - Tue, Dec 23rd 2014 |
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Still problem...
[kmh603@jarvis ~/nwchem]$ ~/programs/Nwchem-6.5/bin/LINUX64/nwchem simple.nw
argument 1 = simple.nw
======================== echo of input deck ========================
start simple
echo
geometry noautosym units angstrom
O -0.702196054 -0.056060256 0.009942262
H -1.022193224 0.846775782 -0.011488714
H 0.257521062 0.042121496 0.005218999
O 2.220871067 0.026716792 0.000620476
H 2.597492682 -0.411663274 0.766744858
H 2.593135384 -0.449496183 -0.744782026
end
memory 1000 mb
charge 0
BASIS SPHERICAL
O library aug-cc-pvqz
H library aug-cc-pvqz
end
DFT
XC XPBE96 CPBE96
END
TASK DFT energy
====================================================================
could not open a file in scratch directory:
------------------------------------------------------------------------
Fatal Error: scratch directory not accessible 911
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
0: TASK DFT energy
------------------------------------------------------------------------
------------------------------------------------------------------------
There is an error in the input file
------------------------------------------------------------------------
For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation
For further details see manual section:
0:Fatal Error: scratch directory not accessible:Received an Error in Communication
application called MPI_Abort(comm=0x84000000, 911) - process 0
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Clicked A Few Times
Threads 5
Posts 11
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| 6:03:47 AM PST - Wed, Jan 28th 2015 |
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Access authority problem
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After some tests, I've found that the problem I told you may be due to some access authority issues.
If I run the program as a root ID, NWChem successfully runs.
However, when I run the program as my own ID, NWChem fails to run.
Even though I chmod 777 to the directories where input and scratch folders are, NWChem fails to run.
If you think you need additional information to solve, please let me know.
Thanks in advance.
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Clicked A Few Times
Threads 5
Posts 11
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| 5:39:27 PM PST - Wed, Feb 11th 2015 |
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Maybe there's some problems with OS.
The same problem occurs in other servers using the RedHat 6.4, while they were successful to run NWChem using the RedHat 5.x and 6.1.
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