From NWChem
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| 8:08:13 AM PDT - Sun, Sep 30th 2018 |
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Greetings!
I am attempting to use Rangsiman Ketkaew's Automatic-NWChem-Compile.sh. I have followed the directions detailed at https://github.com/rangsimanketkaew/NWChem#nwchem-auto-compilation:
1) sudo apt-get install python-dev gfortran libopenblas-dev libopenmpi-dev openmpi-bin tcsh make
2) wget https://github.com/nwchemgit/nwchem/releases/download/6.8.1-release/nwchem-6.8.1-release.r...
3) tar -xvf nwchem-6.8.1-release.revision-v6.8-133-ge032219-src.2018-06-14.tar.bz2
4) wget https://raw.githubusercontent.com/rangsimanketkaew/NWChem/master/Automatic-NWChem-Compile....
5) chmod 755 Automatic-NWChem-Compile.sh
6) ./Automatic-NWChem-Compile.sh, which yielded
*********** Automatic NWChem Compilation ***********
1) Check MPI Architecture 4) Download NWChem 6.8.1
2) Compile NWChem 5) Author & Contact
3) Create Resource file 6) Exit Program
Enter Your Choice: 1
- Linux distribution version : UBUNTU_CODENAME=bionic
- MPI architecture and version : mpirun (Open MPI) 2.1.1
- Fortran Compiler libraries : -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
Enter Your Choice: 2
Enter absolute path of NWChem source code, e.g. /home/rangsiman/nwchem-6.8.1/: /home/doug/Programs/nwchem-6.8.1
Enter version of Python you are using, e.g. 2.6: 2.7
Enter absolute path of Python directory, e.g. /usr/: /usr
=========================================================
Install NWChem version 6.8.1 with Message Passing Interface (MPI)
Configuration compilation has been saved.
Please check /home/doug/Programs/configure_nwchem_compile.sh
=========================================================
Enter YES to start compiling: YES
Start to compile NWChem ...
Building NWChem executable ... This will take 20-30 minutes.
Please do not close this terminal.
-------------------------------------------------------------
ERROR: Program compile failed! nwchem excutable not found.
Check following files to view Log.
/home/doug/Programs/nwchem-6.8.1/src/compile-config.log
/home/doug/Programs/nwchem-6.8.1/src/compile-64_to_32.log
/home/doug/Programs/nwchem-6.8.1/src/compile-make-nwchem.log
Please look at the end of LOG file to see error message.
You can consult NWChem developer at http://www.nwchem-sw.org/index.php/Special:AWCforum
As this website is not allowing uploads, the contents of the first set of .log files will be added as "responses," otherwise this post is too large.
The end of compile-make-nwchem.log contains "GNUmakefile:105: recipe for target 'libraries' failed" followed by "make: *** [libraries] Error 1," which https://github.com/rangsimanketkaew/NWChem#nwchem-auto-compilation lists as an Error with this Fix: "Check the suitable MPI libraries that you can use. Run the script and press [1] or run following command mpif90 -show." Running the script and pressing [1] I did and recorded above. Issuing "mpif90 -show" displays
gfortran -I/usr/lib/x86_64-linux-gnu/openmpi/include -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
As requested in a related post, "which mpif90" was issued and displayed
/usr/bin/mpif90
In that same post, unsetting MPI_INCLUDE, MPI_LIB, and LIBMPI was requested. Doing so and then re-executing Automatic-NWChem-Compile.sh produced the same results in the terminal window as displayed above. The four .log files changed and the contents of this second set of .log files will also be added as "responses."
My thought is that the following, from config.log, is the key to solving this problem:
configure:6532: checking whether a simple C MPI program compiles
configure:6538: cc -c -I/include -I/usr/include conftest.c >&5
conftest.c:32:10: fatal error: mpi.h: No such file or directory
#include <mpi.h>
This file, mpi.h, is not found anywhere in /home/doug/Programs/nwchem-6.8.1. It is found in /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi, and so, perhaps, this path needs to be included in the compile command. But, using this Automatic-NWChem-Compile.sh construct, I do not presently see how to do this.
Thanks for your help!
P.S. My apologies for my failed post of last night, when I tried to include the contents of the .log files; I did not realize it would still show up.
P.P.S. I cannot see how to respond to my own post. Perhaps this forum does not allow this? Bother!
P.P.P.S. Problem solved! I also found mpi.h in /usr/include/mpi, so I replaced
export MPI_INCLUDE=${MPI_LOC}/include
in Automatic-NWChem-Compile.sh with
export MPI_INCLUDE=${MPI_LOC}/usr/include/mpi
I made this change because of this line in config.log
configure:6538: cc -c -I/include -I/usr/include conftest.c >&5
where only "/include" appears, consistent with how it was being set in Automatic-NWChem-Compile.sh. So I changed the path to where mpi.h is found on my installation (/usr/include/mpi), and -- voila! -- " Congratulations! NWChem has been compiled successfully."
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Edited On 5:53:51 PM PDT - Sun, Sep 30th 2018 by Dafemec
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| 10:46:02 AM PST - Wed, Nov 7th 2018 |
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Dafemec,
can you advise on the success of the bionic packages, and suggest what i need to do to fix?
8:03:43 AM PST - Wed, Nov 7th 2018
After installing ubuntu, i used sudo apt install nwchem, successfully. The program runs when sudo is used, and fails when it does not. When i try to use mpirun, it warns not to do that with sudo
platform windows 10 with Windows subsytem for Linux and ubuntu installed
1) Do i need to go back, uninstall nwchem and set environment variables before running sudo apt install nwchem to be able to use MPIRUN
2) Is MPI already installed and i need to change a setting?
3) can i run MIPRUN as sudo- all i am using ubuntu for is nwchem
I cannot match online content with this particular setup. A highlevel order of operations would be appreciated
thanks
Robert
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