[Wien] somethint about the symmetry in the struct file

[姜若诗]

Hello,I want to ask something about the symmetry matrix in the case.struct.
If I change the order of the symmetry matrix in the case.struct.  For example, 
the first matrix is not unitary,I change the eighth matrix and the first matrix 
in the case.struct_st in ordet to make sure the first one is unitary,then I run 
it.Will it have some influence to my result?
 Wish your reply.
 Sincerely
  Jasmine
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

Re: [Wien] Issues with parallel runs

[Gavin Abo]

As Prof. Marks hinted at, it looks to me that mpirun is properly set in 
your PATH of your current terminal such that mpirun works.


However, when you run "run_lapw -p", probably when that script executes 
the lapw1para_lapw script, the program is probably then doing an ssh 
into the nodes you have set in your .machines file. It is on the nodes 
that that mpirun command probably cannot be found.


You can likely test if that is the case in the terminal by trying 
commands like:


ssh localhost
which mpirun
exit

where localhost above should be replaced by the hostname (or ip address) 
to one of your local (e.g. https://en.wikipedia.org/wiki/Localhost ) or 
remote nodes that you have used in your hand edited .machines file.  Or 
if your .machines file is created automatically on the fly by your job 
script [ http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html ], 
which is usually the case for the clusters needed and used for mpi 
parallel calculations, you should be able find the hostnames in the 
.machines file that it tried to use for the calculation when it failed.


If you set the base path to mpirun in the PATH of your .bashrc (or 
.cshrc) [e.g., 
https://www.open-mpi.org/faq/?category=running#adding-ompi-to-path ] and 
your system pushes that out to all nodes, that might resolve the 
problem.  If you are using a job script, depending on your queuing 
system, you might have to add an option to push the environment to the 
nodes [ 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15985.html 
].


If your system doesn't access remote nodes with ssh, see section "11.4 
Environment Variables" in the WIEN2k 18.2 userguide 
[http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf] 
about setting "USE_REMOTE 0" in parallel_options so that it does not use 
ssh.


Depending on the hardware specifications of your workstation, keep in 
mind as mentioned in the list before if it is a general-purpose 
computer, and not a high performance computing (HPC) cluster [ 
https://en.wikipedia.org/wiki/Supercomputer ], that k-point parallel 
might work better than mpi parallel for certain computer systems (or 
calculation cases):


http://susi.theochem.tuwien.ac.at/reg_user/benchmark/
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03793.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08301.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13632.html
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09334.html

On 1/10/2019 12:44 PM, Laurence Marks wrote:
Most probably you forgot to export your PATH (e.g. from bash do 
"export PATH") so the information is not making it beyond your shell. 
You might have a bad csh/tcsh. Try adding "which lapw1_mpi" to 
$WIENROOT/parallel_options, and check that file has correct setenv 
for  WIEN_MPIRUN.


On Thu, Jan 10, 2019 at 12:00 PM Matthew D Redell 
mailto:mrede...@binghamton.edu>> wrote:


Hello,

I am running WIEN2k_2018.2 on CentOs7 and have come across the
following problem that I cannot seem to resolve.

After successfully initializing the calculation and setting up the
.machines for a single host (local workstation), I run: run_lapw -p

lapw0 ends fine, but the lapw1 returns
bash: mpirun: command not found

The same error occurs if I just try
x lapw1 -p

However, which mpirun
returns
/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpirun

I also did a little troubleshooting to see if I could run lapw1 in
parallel via

mpirun -n 4 lapw1_mpi lapw1_1.def


which ran without any issues. Also, checking more…
grep MPIRUN $WIENROOT/WIEN2k_OPTIONS
returns
current:MPIRUN:mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_

So, the only possibility I am able to deduce is that either the
run_lapw script or the lapw1para script is not locating the mpirun
command, but I do not know how to begin sorting out this issue.
Any help would be greatly appreciated.

Best,
Matt


Matthew D Redell
/Graduate Student/Teaching Assistant/
/Department of Physics, Applied Physics, and Astronomy/
*Binghamton University-State University of New York*
E-mail: mrede...@binghamton.edu 
Office: SN-2011D








--
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what 
nobody else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu  ; 
Corrosion in 4D: MURI4D.numis.northwestern.edu 

Partner of the CFW 100% program for gender equity, 
www.cfw.org/100-percent 

Co-Editor, Acta Cryst A
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  

Re: [Wien] Issues with parallel runs

[Laurence Marks]

Most probably you forgot to export your PATH (e.g. from bash do "export
PATH") so the information is not making it beyond your shell. You might
have a bad csh/tcsh. Try adding "which lapw1_mpi" to
$WIENROOT/parallel_options, and check that file has correct setenv for
WIEN_MPIRUN.

On Thu, Jan 10, 2019 at 12:00 PM Matthew D Redell 
wrote:

> Hello,
>
> I am running WIEN2k_2018.2 on CentOs7 and have come across the following
> problem that I cannot seem to resolve.
>
> After successfully initializing the calculation and setting up the
> .machines for a single host (local workstation), I run: run_lapw -p
>
> lapw0 ends fine, but the lapw1 returns
> bash: mpirun: command not found
>
> The same error occurs if I just try
> x lapw1 -p
>
> However, which mpirun
> returns
> /opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpirun
>
> I also did a little troubleshooting to see if I could run lapw1 in
> parallel via
>
> mpirun -n 4 lapw1_mpi lapw1_1.def
>
>
> which ran without any issues. Also, checking more…
> grep MPIRUN $WIENROOT/WIEN2k_OPTIONS
> returns
> current:MPIRUN:mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_
>
> So, the only possibility I am able to deduce is that either the run_lapw
> script or the lapw1para script is not locating the mpirun command, but I do
> not know how to begin sorting out this issue. Any help would be greatly
> appreciated.
>
> Best,
> Matt
>
> 
> Matthew D Redell
> *Graduate Student/Teaching Assistant*
> *Department of Physics, Applied Physics, and Astronomy*
> *Binghamton University-State University of New York*
> E-mail: mrede...@binghamton.edu 
> Office: SN-2011D
>
>
>
>
>
>
>

-- 
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu ; Corrosion in 4D: MURI4D.numis.northwestern.edu
Partner of the CFW 100% program for gender equity, www.cfw.org/100-percent
Co-Editor, Acta Cryst A
___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

[Wien] Issues with parallel runs

[Matthew D Redell]

Hello,

I am running WIEN2k_2018.2 on CentOs7 and have come across the following 
problem that I cannot seem to resolve.

After successfully initializing the calculation and setting up the .machines 
for a single host (local workstation), I run: run_lapw -p

lapw0 ends fine, but the lapw1 returns
bash: mpirun: command not found

The same error occurs if I just try 
x lapw1 -p

However, which mpirun
returns 
/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpirun

I also did a little troubleshooting to see if I could run lapw1 in parallel via
mpirun -n 4 lapw1_mpi lapw1_1.def

which ran without any issues. Also, checking more…
grep MPIRUN $WIENROOT/WIEN2k_OPTIONS
returns
current:MPIRUN:mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_

So, the only possibility I am able to deduce is that either the run_lapw script 
or the lapw1para script is not locating the mpirun command, but I do not know 
how to begin sorting out this issue. Any help would be greatly appreciated.

Best,
Matt


Matthew D Redell
Graduate Student/Teaching Assistant
Department of Physics, Applied Physics, and Astronomy
Binghamton University-State University of New York
E-mail: mrede...@binghamton.edu
Office: SN-2011D






___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

Re: [Wien] Possible clash between different libiomp5.so library file

[Lawal Mohammed]

Thanks a lot Prof. L. Mark, I take your advice.
Actually I did nothing, because the system admin handled the issue after your 
first letter.Now, the issue of libiomp5.so is solved, I was told about an issue 
between the wien2k and intel_2015.
With kind regards.
Lawal 

 

On Thursday, January 10, 2019, 3:38:03 PM GMT+8, Laurence Marks 
 wrote:  
 
 Read the ouput from "ifort --help", or "man ifort". Learn!

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody else 
has thought", Albert Szent-Gyorgi
www.numis.northwestern.edu
On Wed, Jan 9, 2019, 23:21 Lawal Mohammed   (0x7fff3cfa7000)        libiomp5.so => 
/software/intel2015-1/composer_xe_2015.3.187/compiler/lib/intel64/libiomp5.so 
(0x2b8340b5f000)        libpthread.so.0 => /lib64/libpthread.so.0 
(0x2b8340e9f000)        libm.so.6 => /lib64/libm.so.6 (0x2b83410bf000)  
      libdl.so.2 => /lib64/libdl.so.2 (0x2b83413c7000)        libc.so.6 => 
/lib64/libc.so.6 (0x2b83415cf000)        /lib64/ld-linux-x86-64.so.2 
(0x2b8340937000)        libgcc_s.so.1 => /lib64/libgcc_s.so.1 
(0x2b8341997000)
The compilation and execution was done using composer_xe_2015.3.187, 
libiomp5.so seems to be in right directory. Please which part of compilation 
option should I edit, and I couldn't figure out what you mean by static 
compilation in this case. 
The system admin is interested, so I have already forward the link to this 
thread to him/them. 
With kind regards
Lawal



On Thursday, January 10, 2019, 10:17:23 AM GMT+8, Laurence Marks 
 wrote:

Try "ldd lapw0" to see what shared libraries are being used, then edit your 
compilation options to do static compilation. Depending upon what compiler your 
have the options will change; do "ifort --help | more" or "ifort --help > 
Fort.txt" and read (or gfortran, etc).
At least for the non-mpi you can build lapw0 & others without any shared 
libraries. I have never seen this fail, but it might.

On Wed, Jan 9, 2019, 19:58 Lawal Mohammed    lapw0  -p   (09:48:12) starting parallel lapw0 at Thu Jan 10 09:48:12 CST 
>2019 .machine0 : processorsrunning lapw0 in single mode0.022u 0.036s 
>0:00.08 62.5%     0+0k 0+56io 0pf+0werror: command   
>/software/wien2k-18.2/lapw0para lapw0.def   failed>   stop error
In the output file the error is:lapw0: relocation error: lapw0: symbol 
kmp_aligned_malloc, version VERSION not defined in file libiomp5.so with link 
time reference
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory
Many thanks to Gavin for pointing out that the error was due to clash between 
other libraries with the  Intel Fortran library. However, after I reported the 
issue, system admin confirmed that the environmental variables was okay. Any 
help to rectify this issue is highly appreciated.
I will provide addition information if needed.
Thanks alot for your time.With kind regards.
Lawal


___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
  ___
Wien mailing list
Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html