Running NWChem in parallel

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Hello,

I installed NWChem from the Ubuntu Software Center. However, after following http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id524/#post_1858 and http://www.nwchem-sw.org/index.php/Release61:Running I am unable to run the program in parallel on my Ubuntu laptop.

When I try "mpirun -np 2 nwchem h2.nw > h2.out"

I get this printed to standard error:

"rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
 0: ARMCI aborting 0 (0).
0: ARMCI aborting 0 (0)."

and the output says
"Last System Error Message from Task 0:: No such file or directory
 0: ARMCI aborting 0 (0).
system error message: Invalid argument"

and the output file says "nproc = 1"

I have the .bashrc file settings

"export NWCHEM_TOP=/home/dave/nwchem
export NWCHEM_TARGET=LINUX64
export USE_MPI="y" #Set to "y" to indicate that NWChem should be compiled with MPI
export USE_MPIF="y" #Set to "y" for the NWPW module to use fortran-bindings of MPI (Generally set when USE_MPI is set)
export USE_MPIF4="y" #Set to "y" for the NWPW module to use Integer*4 fortran-bindings of MPI. (Generally set when USE_MPI is set on most platforms)
export LIBMPI="-lmpich -lopa -lmpl -lrt -lpthread" #Name of the MPI library that should be linked with -l (eg. -lmpich)
export MPI_LIB="/usr/mpich-mpd/bin/mpirun".

With all of that said, I have two questions:

1. How can I get this to run in parallel?
2. Since I followed a non-standard install, how can I update to 6.1.1?

Thanks,
-DC

  • Bert Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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The version at available at the Ubuntu is a serial binary I believe (i.e. not build on top of MPI). However, by default the code gets build on top of TCGMSG, so you might try running it following http://www.nwchem-sw.org/index.php/Release61:Running#Parallel_execution_on_UNIX-based_para...

Alternatively you can download the source from our website and build your own version with MPI.

Bert


Quote:Hhg Oct 5th 6:23 pm
Hello,

I installed NWChem from the Ubuntu Software Center. However, after following http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id524/#post_1858 and http://www.nwchem-sw.org/index.php/Release61:Running I am unable to run the program in parallel on my Ubuntu laptop.

When I try "mpirun -np 2 nwchem h2.nw > h2.out"

I get this printed to standard error:

"rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
rtdb_seq_get: size error "geometry:names" in ./h2.db: info=42, db=15
 0: ARMCI aborting 0 (0).
0: ARMCI aborting 0 (0)."

and the output says
"Last System Error Message from Task 0:: No such file or directory
 0: ARMCI aborting 0 (0).
system error message: Invalid argument"

and the output file says "nproc = 1"

I have the .bashrc file settings

"export NWCHEM_TOP=/home/dave/nwchem
export NWCHEM_TARGET=LINUX64
export USE_MPI="y" #Set to "y" to indicate that NWChem should be compiled with MPI
export USE_MPIF="y" #Set to "y" for the NWPW module to use fortran-bindings of MPI (Generally set when USE_MPI is set)
export USE_MPIF4="y" #Set to "y" for the NWPW module to use Integer*4 fortran-bindings of MPI. (Generally set when USE_MPI is set on most platforms)
export LIBMPI="-lmpich -lopa -lmpl -lrt -lpthread" #Name of the MPI library that should be linked with -l (eg. -lmpich)
export MPI_LIB="/usr/mpich-mpd/bin/mpirun".

With all of that said, I have two questions:

1. How can I get this to run in parallel?
2. Since I followed a non-standard install, how can I update to 6.1.1?

Thanks,
-DC

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Threads 7
Posts 1086
Debian packages linked with MPI
DC,
Another option you might want to consider is to install the Debian NWChem binary packages under Ubuntu, since
the are linked against MPI.
I have tried them under my Ubuntu 12.04 install and they seem to work for simple tests.
These are the packages I have download and installed from debian unstable (a.k.a sid)
http://ftp.us.debian.org/debian/pool/main/n/nwchem/nwchem-data_6.1-4_all.deb
http://ftp.us.debian.org/debian/pool/main/n/nwchem/nwchem_6.1-4_amd64.deb

Cheers, Edo

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Posts 13
Hi Bert,

I tried making the file nwchem.p which is written:

"1000 zip.chem.rochester.edu 4 /usr/bin/nwchem /home/dave/nwchem". I got the userid through the "id" command.

I executed with:

"parallel nwchem optbenzene.nw" but nothing happens. Is this how to set up and use the process group file?

When I try "mpiexec -np 2 nwchem optbenzene.nw > 2.out"

it runs and shows two NWChem processes in top but also shows "nproc = 1" in the output file. The process "hydra_pmi_proxy" runs constantly at 100% whether I am running nwchem or not. I can't kill it with the "kill" command.

and to Edoapra,

I clicked on the links you provided and I got the message "Dependency is not satisfiable: nwchem-data (=6.1-4)".

This is like a comedy of errors lol.

Thanks so much for your assistance!
-Dave

Forum Vet
Threads 7
Posts 1086
Quote:Hhg Oct 5th 12:43 pm


I clicked on the links you provided and I got the message "Dependency is not satisfiable: nwchem-data (=6.1-4)".


Yes, you need to satisfy the nwchem-date 6-1.4 dependence by
1) first to install the nwchem-data package fron
http://ftp.us.debian.org/debian/pool/main/n/nwchem/nwchem-data_6.1-4_all.deb
then
2) second
http://ftp.us.debian.org/debian/pool/main/n/nwchem/nwchem_6.1-4_amd64.deb

Clicked A Few Times
Threads 5
Posts 13
Edoapra,

thanks so much! I finally figured it out. The solution is to

1. sudo dpkg -i nwchem-data_6.1-4_all.deb
2. sudo dpkg -i nwchem_6.1-4_amd64.deb

Note that step 2 produces an error. This can be corrected with sudo dpkg-reconfigure packagename and opening/closing the ubuntu software center.

I am now able to run my calculations about 4x faster than before. Thanks so much!


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