Re: [Wien] MPI Error while running lapw0_mpi

[Laurence Marks]

As Peter said, try running on just 4 cores. There are some things that can
go wrong if you use many mpi for small problems.

Beyond that, please execute "ulimit -a" at a terminal. It is also good to
run it remotely in a job. I want to find out whether you have no rights to
set limits but they are large, or that they have been set for you at some
small value. The second case may be a deep problem where you will have to
work with the admin of the computer, and we cannot help. (If the limits are
large the messages reporting that you cannot set them can be ignored.)

N.B. read the ulimit man page.

--
Professor Laurence Marks
Department of Materials Science and Engineering, Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody
else has thought" Albert Szent-Györgyi

On Wed, Mar 23, 2022, 5:54 AM Peter Blaha 
wrote:

> Try to run the lapw0_mpi on 4 cores only.
>
> Am 3/23/22 um 11:48 schrieb venky ch:
> >
> > Dear Prof. Marks and Prof. Blaha,
> >
> > Thanks for your quick responses. The answers are as follows,
> >
> > a) Is this a supercomputer, a lab cluster or your cluster?
> >
> > Ans: It is a supercomputer
> >
> > b) Did you set it up or did someone else?
> >
> > Ans: I haven't set up these ulimits.
> >
> > c) Do you have root/su rights?
> >
> > Ans:  I don't have root/su rights
> >
> > What case is it, that you run it on 32 cores ?  How many atoms ??
> >
> > Ans: The case.struct has 3 atoms and for the total of 1000 k-points, it
> > gave 102 reduced k-points. As I want to test the running parallel
> > calculations, I just took a small system with more k-points.
> >
> > thanks and regards
> > venkatesh
> >
>
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Re: [Wien] MPI Error while running lapw0_mpi

[Peter Blaha]

Try to run the lapw0_mpi on 4 cores only.

Am 3/23/22 um 11:48 schrieb venky ch:


Dear Prof. Marks and Prof. Blaha,

Thanks for your quick responses. The answers are as follows,

a) Is this a supercomputer, a lab cluster or your cluster?

Ans: It is a supercomputer

b) Did you set it up or did someone else?

Ans: I haven't set up these ulimits.

c) Do you have root/su rights?

Ans:  I don't have root/su rights

What case is it, that you run it on 32 cores ?  How many atoms ??

Ans: The case.struct has 3 atoms and for the total of 1000 k-points, it 
gave 102 reduced k-points. As I want to test the running parallel 
calculations, I just took a small system with more k-points.


thanks and regards
venkatesh


On Wed, Mar 23, 2022 at 2:12 PM Laurence Marks > wrote:


There are many things wrong, but let's start with the critical one
-- ulimit.
a) Is this a supercomputer, a lab cluster or your cluster?
b) Did you set it up or did someone else?
c) Do you have root/su rights?

Someone has set limits in such a way that it is interfering with the
calculations. It used to be more common to see this, but it has been
some years since I have seen it. You can look at, for instance,
https://ss64.com/bash/ulimit.html .

The best solution is to find out how these got set and remove them.
For that you need to do some local research.

--
Professor Laurence Marks
Department of Materials Science and Engineering, Northwestern University
www.numis.northwestern.edu 
"Research is to see what everybody else has seen, and to think what
nobody else has thought" Albert Szent-Györgyi

On Wed, Mar 23, 2022, 3:31 AM venky ch mailto:chvenkatesh...@gmail.com>> wrote:

Dear Wien2k users,

I have successfully installed the wien2k.21 version in the HPC
cluster. However, while running a test calculation, I am getting
the following error so that the lapw0_mpi crashed.

=

/home/proj/21/phyvech/.bashrc: line 43: ulimit: stack size:
cannot modify limit: Operation not permitted
/home/proj/21/phyvech/.bashrc: line 43: ulimit: stack size:
cannot modify limit: Operation not permitted
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
setrlimit(): WARNING: Cannot raise stack limit, continuing:
Invalid argument
Abort(744562703) on node 1 (rank 1 in comm 0): Fatal error in
PMPI_Bcast: Other MPI error, error stack:
PMPI_Bcast(432).:
MPI_Bcast(buf=0x7ffd8f8d359c, count=1, MPI_INTEGER, root=0,
comm=MPI_COMM_WORLD) failed
PMPI_Bcast(418).:
MPIDI_Bcast_intra_composition_gamma(391):
MPIDI_NM_mpi_bcast(153).:
MPIR_Bcast_intra_tree(219)..: Failure during collective
MPIR_Bcast_intra_tree(211)..:
MPIR_Bcast_intra_tree_generic(176)..: Failure during collective
[1]    Exit 15                       mpirun -np 32 -machinefile
.machine0 */home/proj/21/phyvech/soft/win2k2/lapw0_mpi lapw0.def
 >> .time00*
cat: No match.
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory

=

the .machines file is

=== for 102 reduced k-points =

#
lapw0:node16:16 node22:16
51:node16:16
51:node22:16
granularity:1
extrafine:1

Re: [Wien] MPI Error while running lapw0_mpi

[venky ch]

Dear Prof. Marks and Prof. Blaha,

Thanks for your quick responses. The answers are as follows,

a) Is this a supercomputer, a lab cluster or your cluster?

Ans: It is a supercomputer

b) Did you set it up or did someone else?

Ans: I haven't set up these ulimits.

c) Do you have root/su rights?

Ans:  I don't have root/su rights

What case is it, that you run it on 32 cores ?  How many atoms ??

Ans: The case.struct has 3 atoms and for the total of 1000 k-points, it
gave 102 reduced k-points. As I want to test the running parallel
calculations, I just took a small system with more k-points.

thanks and regards
venkatesh


On Wed, Mar 23, 2022 at 2:12 PM Laurence Marks 
wrote:

> There are many things wrong, but let's start with the critical one --
> ulimit.
> a) Is this a supercomputer, a lab cluster or your cluster?
> b) Did you set it up or did someone else?
> c) Do you have root/su rights?
>
> Someone has set limits in such a way that it is interfering with the
> calculations. It used to be more common to see this, but it has been some
> years since I have seen it. You can look at, for instance,
> https://ss64.com/bash/ulimit.html.
>
> The best solution is to find out how these got set and remove them. For
> that you need to do some local research.
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering, Northwestern University
> www.numis.northwestern.edu
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought" Albert Szent-Györgyi
>
> On Wed, Mar 23, 2022, 3:31 AM venky ch  wrote:
>
>> Dear Wien2k users,
>>
>> I have successfully installed the wien2k.21 version in the HPC cluster.
>> However, while running a test calculation, I am getting the following error
>> so that the lapw0_mpi crashed.
>>
>> =
>>
>> /home/proj/21/phyvech/.bashrc: line 43: ulimit: stack size: cannot modify
>> limit: Operation not permitted
>> /home/proj/21/phyvech/.bashrc: line 43: ulimit: stack size: cannot modify
>> limit: Operation not permitted
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
>> argument
>> Abort(744562703) on node 1 (rank 1 in comm 0): Fatal error in PMPI_Bcast:
>> Other MPI error, error stack:
>> PMPI_Bcast(432).: MPI_Bcast(buf=0x7ffd8f8d359c,
>> count=1, MPI_INTEGER, root=0, comm=MPI_COMM_WORLD) failed
>> PMPI_Bcast(418).:
>> MPIDI_Bcast_intra_composition_gamma(391):
>> MPIDI_NM_mpi_bcast(153).:
>> MPIR_Bcast_intra_tree(219)..: Failure during collective
>> MPIR_Bcast_intra_tree(211)..:
>> MPIR_Bcast_intra_tree_generic(176)..: Failure during collective
>> [1]Exit 15   mpirun -np 32 -machinefile .machine0 
>> */home/proj/21/phyvech/soft/win2k2/lapw0_mpi
>> lapw0.def >> .time00*
>> cat: No match.
>> grep: *scf1*: No such file or directory
>> grep: lapw2*.error: No such file or directory
>>
>> =
>>
>> the .machines file is
>>
>> === for 102 reduced k-points =
>>
>> #
>> lapw0:node16:16 node22:16
>> 51:node16:16
>> 51:node22:16
>> granularity:1
>> extrafine:1
>>
>> 
>>
>> "export OMP_NUM_THREADS=1" has been used in the job submission script.
>>
>> "run_lapw -p -NI -i 400 -ec 0.1 -cc 0.0001" has been used to start
>> the parallel calculations in available nodes.
>>
>> Can someone please explain to me where I am going wrong here. Thanks in
>> advance.
>>
>> Regards,
>> Venkatesh
>> Physics department
>> IISc Bangalore, INDIA
>>
>> ___
>> Wien mailing list
>> Wien@zeus.theochem.tuwien.ac.at
>>
>> 

Re: [Wien] MPI Error while running lapw0_mpi

[Peter Blaha]

What case is it, that you run it on 32 cores ?  How many atoms ??


Remember:   more cores does not always mean faster, in fact it could 
also mean crash or MUCH slower 



Please read the parallelization section of the UG.


Am 23.03.2022 um 09:31 schrieb venky ch:

Dear Wien2k users,

I have successfully installed the wien2k.21 version in the HPC 
cluster. However, while running a test calculation, I am getting the 
following error so that the lapw0_mpi crashed.


=

/home/proj/21/phyvech/.bashrc: line 43: ulimit: stack size: cannot 
modify limit: Operation not permitted
/home/proj/21/phyvech/.bashrc: line 43: ulimit: stack size: cannot 
modify limit: Operation not permitted
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid 
argument
Abort(744562703) on node 1 (rank 1 in comm 0): Fatal error in 
PMPI_Bcast: Other MPI error, error stack:
PMPI_Bcast(432).: 
MPI_Bcast(buf=0x7ffd8f8d359c, count=1, MPI_INTEGER, root=0, 
comm=MPI_COMM_WORLD) failed

PMPI_Bcast(418).:
MPIDI_Bcast_intra_composition_gamma(391):
MPIDI_NM_mpi_bcast(153).:
MPIR_Bcast_intra_tree(219)..: Failure during collective
MPIR_Bcast_intra_tree(211)..:
MPIR_Bcast_intra_tree_generic(176)..: Failure during collective
[1]    Exit 15                       mpirun -np 32 -machinefile 
.machine0 */home/proj/21/phyvech/soft/win2k2/lapw0_mpi lapw0.def >> 
.time00*

cat: No match.
grep: *scf1*: No such file or directory
grep: lapw2*.error: No such file or directory

=

the .machines file is

=== for 102 reduced k-points =

#
lapw0:node16:16 node22:16
51:node16:16
51:node22:16
granularity:1
extrafine:1



"export OMP_NUM_THREADS=1" has been used in the job submission script.

"run_lapw -p -NI -i 400 -ec 0.1 -cc 0.0001" has been used to start 
the parallel calculations in available nodes.


Can someone please explain to me where I am going wrong here. Thanks 
in advance.


Regards,
Venkatesh
Physics department
IISc Bangalore, INDIA


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--
---
Peter Blaha,  Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email:peter.bl...@tuwien.ac.at   
WWW:http://www.imc.tuwien.ac.at   WIEN2k:http://www.wien2k.at

-
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Re: [Wien] MPI Error while running lapw0_mpi

[Laurence Marks]

There are many things wrong, but let's start with the critical one --
ulimit.
a) Is this a supercomputer, a lab cluster or your cluster?
b) Did you set it up or did someone else?
c) Do you have root/su rights?

Someone has set limits in such a way that it is interfering with the
calculations. It used to be more common to see this, but it has been some
years since I have seen it. You can look at, for instance,
https://ss64.com/bash/ulimit.html.

The best solution is to find out how these got set and remove them. For
that you need to do some local research.

--
Professor Laurence Marks
Department of Materials Science and Engineering, Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody
else has thought" Albert Szent-Györgyi

On Wed, Mar 23, 2022, 3:31 AM venky ch  wrote:

> Dear Wien2k users,
>
> I have successfully installed the wien2k.21 version in the HPC cluster.
> However, while running a test calculation, I am getting the following error
> so that the lapw0_mpi crashed.
>
> =
>
> /home/proj/21/phyvech/.bashrc: line 43: ulimit: stack size: cannot modify
> limit: Operation not permitted
> /home/proj/21/phyvech/.bashrc: line 43: ulimit: stack size: cannot modify
> limit: Operation not permitted
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> setrlimit(): WARNING: Cannot raise stack limit, continuing: Invalid
> argument
> Abort(744562703) on node 1 (rank 1 in comm 0): Fatal error in PMPI_Bcast:
> Other MPI error, error stack:
> PMPI_Bcast(432).: MPI_Bcast(buf=0x7ffd8f8d359c,
> count=1, MPI_INTEGER, root=0, comm=MPI_COMM_WORLD) failed
> PMPI_Bcast(418).:
> MPIDI_Bcast_intra_composition_gamma(391):
> MPIDI_NM_mpi_bcast(153).:
> MPIR_Bcast_intra_tree(219)..: Failure during collective
> MPIR_Bcast_intra_tree(211)..:
> MPIR_Bcast_intra_tree_generic(176)..: Failure during collective
> [1]Exit 15   mpirun -np 32 -machinefile .machine0 
> */home/proj/21/phyvech/soft/win2k2/lapw0_mpi
> lapw0.def >> .time00*
> cat: No match.
> grep: *scf1*: No such file or directory
> grep: lapw2*.error: No such file or directory
>
> =
>
> the .machines file is
>
> === for 102 reduced k-points =
>
> #
> lapw0:node16:16 node22:16
> 51:node16:16
> 51:node22:16
> granularity:1
> extrafine:1
>
> 
>
> "export OMP_NUM_THREADS=1" has been used in the job submission script.
>
> "run_lapw -p -NI -i 400 -ec 0.1 -cc 0.0001" has been used to start the
> parallel calculations in available nodes.
>
> Can someone please explain to me where I am going wrong here. Thanks in
> advance.
>
> Regards,
> Venkatesh
> Physics department
> IISc Bangalore, INDIA
>
> ___
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Re: [Wien] MPI Error

[Peter Blaha]

Definitely, it has nothing to do with MPI_REMOTE.

apparently, your ssh setup does not transfer the "environment".

There are 2 solutions:

If you want to run k-parallel only on one node, simply put
USE_REMOTE=0   in parallel_options. However, with this you are not able 
to use more nodes in one k-parallel job.


configure your own config files for   ssh/sshd  in .ssh/config (and I 
believe .sshd/config)

You can direct ssh to send your environment and the sshd to accept it.
The default behavior is configured by the sysadmin in 
/etc/ssh/ssh_config and sshd_config. These files you cannot change, but 
you can override these settings.
Most likely, you need a   SendEnv PATH   and  AcceptEnv PATH in the 2 
files, maybe some more variables.


See   man ssh_config   and   man sshd_config

Am 19.06.2021 um 12:59 schrieb leila mollabashi:

Dear all WIEN2k users,


The recommended option for  mpi version 2 (all modern mpis) is to set

MPI_REMOTE to zero. The mpirun command will be issued on the original
node, but the lapw1_mpi executables will run as given in .machines.


This should solve your problem.


Now mpi and k-point parallel simultaneously run but k-point parallel 
without mpi does not work using interactive mode or in interactive mode 
by “set mpijob=1” in submit.sh script.  For example, with the following 
.machines file:


1:e2236

1:e2236

1:e2236

1:e2236

the following error appeared:

bash: lapw1: command not found

My question is whether I can use two different installations of wien2k 
for performing two different calculations at the same time?


Sincerely yours,

Leila


On Sat, May 29, 2021 at 7:07 PM Peter Blaha 
mailto:pbl...@theochem.tuwien.ac.at>> wrote:


The difference beteen lapw0para and lapw1para is that
lapw0para always executes mpirun on the original node, lapw1para
maybe not.

The behavior of lapw1para depends on MPI_REMOTE (set in
WIEN2k_parallel_options in w2k21.1 (or parallel_options earlier).
With MPI_REMOTE=1 it will first issue a   ssh nodename and there it
does
the mpirun. This does not work with your settings (probably because you
do not load the modules in your .bashrc (or .cshrc), but only in your
slurm-job and your system does not transfer the environment with ssh.

The recommended option for mpi version 2 (all modern mpis) is to set
MPI_REMOTE to zero. The mpirun command will be issued on the original
node, but the lapw1_mpi executables will run as given in .machines.

This should solve your problem.

Am 29.05.2021 um 08:39 schrieb leila mollabashi:
 > Dear all wien2k users,
 > Following the previous comment referring me to the admin, I
contacted
 > the cluster admin. By the comment of the admin, I recompiled Wien2k
 > successfully using the cluster modules.
 >>Once the blacs problem has been fixed,
 > For example, is the following correct?
 > libmkl_blacs_openmpi_lp64.so =>
 >

/opt/exp_soft/local/generic/intel/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so

 > (0x2b21efe03000)
 >>the next step is to run lapw0 in
 > sequential and parallel mode.
 >>Add:
 > x lapw0     and check the case.output0 and case.scf0 files (copy
them to
 > a different name) as well as the message from the queuing system. ...
 > The “x lapw0” and “mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def” are
 > interactively executed correctly.
 > The “x lapw0 -p” is also correctly executed using the following
 > “.machines” file:
 > lapw0:e0017:4
 >>The same thing could be made with lapw1
 > The “x lapw1” and “mpirun -np 4 $WIENROOT/lapw1_mpi lapw1.def”
are also
 > correctly executed interactively with no problem. But “x lapw1
-p” stops
 > when I use the following “.machines” file:
 > 1:e0017:2
 > 1:e0017:2
 > bash: mpirun: command not found
 > The output files are gathered into https://files.fm/u/7cssehdck

 > >.
 > Would you, please, help me to fix the parallel problem too?
 > Sincerely yours,
 > Leila
 >
 >
 > ___
 > 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

 >

-- 
--

Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300             FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at
    WIEN2k: 

Re: [Wien] MPI Error

[Laurence Marks]

As before, command not found is a PATH problem, nothing to do with Wien2k.

Why do you want many versions? One version can run many jobs in parallel.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Sat, Jun 19, 2021, 06:00 leila mollabashi 
wrote:

> Dear all WIEN2k users,
>
> >The recommended option for mpi version 2 (all modern mpis) is to set
> MPI_REMOTE to zero. The mpirun command will be issued on the original
> node, but the lapw1_mpi executables will run as given in .machines.
>
> >This should solve your problem.
>
> Now mpi and k-point parallel simultaneously run but k-point parallel
> without mpi does not work using interactive mode or in interactive mode  by
> “set mpijob=1” in submit.sh script.  For example, with the following
> .machines file:
>
> 1:e2236
>
> 1:e2236
>
> 1:e2236
>
> 1:e2236
>
> the following error appeared:
>
> bash: lapw1: command not found
>
> My question is whether I can use two different installations of wien2k for
> performing two different calculations at the same time?
>
> Sincerely yours,
>
> Leila
>
>
> On Sat, May 29, 2021 at 7:07 PM Peter Blaha 
> wrote:
>
>> The difference beteen lapw0para and lapw1para is that
>> lapw0para always executes mpirun on the original node, lapw1para maybe
>> not.
>>
>> The behavior of lapw1para depends on MPI_REMOTE (set in
>> WIEN2k_parallel_options in w2k21.1 (or parallel_options earlier).
>> With MPI_REMOTE=1 it will first issue a   ssh nodename and there it does
>> the mpirun. This does not work with your settings (probably because you
>> do not load the modules in your .bashrc (or .cshrc), but only in your
>> slurm-job and your system does not transfer the environment with ssh.
>>
>> The recommended option for mpi version 2 (all modern mpis) is to set
>> MPI_REMOTE to zero. The mpirun command will be issued on the original
>> node, but the lapw1_mpi executables will run as given in .machines.
>>
>> This should solve your problem.
>>
>> Am 29.05.2021 um 08:39 schrieb leila mollabashi:
>> > Dear all wien2k users,
>> > Following the previous comment referring me to the admin, I contacted
>> > the cluster admin. By the comment of the admin, I recompiled Wien2k
>> > successfully using the cluster modules.
>> >>Once the blacs problem has been fixed,
>> > For example, is the following correct?
>> > libmkl_blacs_openmpi_lp64.so =>
>> >
>> /opt/exp_soft/local/generic/intel/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so
>>
>> > (0x2b21efe03000)
>> >>the next step is to run lapw0 in
>> > sequential and parallel mode.
>> >>Add:
>> > x lapw0 and check the case.output0 and case.scf0 files (copy them to
>> > a different name) as well as the message from the queuing system. ...
>> > The “x lapw0” and “mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def” are
>> > interactively executed correctly.
>> > The “x lapw0 -p” is also correctly executed using the following
>> > “.machines” file:
>> > lapw0:e0017:4
>> >>The same thing could be made with lapw1
>> > The “x lapw1” and “mpirun -np 4 $WIENROOT/lapw1_mpi lapw1.def” are also
>> > correctly executed interactively with no problem. But “x lapw1 -p”
>> stops
>> > when I use the following “.machines” file:
>> > 1:e0017:2
>> > 1:e0017:2
>> > bash: mpirun: command not found
>> > The output files are gathered into https://files.fm/u/7cssehdck
>> 
>> > > 
>> >.
>> > Would you, please, help me to fix the parallel problem too?
>> > Sincerely yours,
>> > Leila
>> >
>> >
>> > ___
>> > 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
>> 
>> >
>>
>> --
>> --
>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
>> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
>> 

Re: [Wien] MPI Error

[leila mollabashi]

Dear all WIEN2k users,

>The recommended option for mpi version 2 (all modern mpis) is to set
MPI_REMOTE to zero. The mpirun command will be issued on the original
node, but the lapw1_mpi executables will run as given in .machines.

>This should solve your problem.

Now mpi and k-point parallel simultaneously run but k-point parallel
without mpi does not work using interactive mode or in interactive mode  by
“set mpijob=1” in submit.sh script.  For example, with the following
.machines file:

1:e2236

1:e2236

1:e2236

1:e2236

the following error appeared:

bash: lapw1: command not found

My question is whether I can use two different installations of wien2k for
performing two different calculations at the same time?

Sincerely yours,

Leila


On Sat, May 29, 2021 at 7:07 PM Peter Blaha 
wrote:

> The difference beteen lapw0para and lapw1para is that
> lapw0para always executes mpirun on the original node, lapw1para maybe not.
>
> The behavior of lapw1para depends on MPI_REMOTE (set in
> WIEN2k_parallel_options in w2k21.1 (or parallel_options earlier).
> With MPI_REMOTE=1 it will first issue a   ssh nodename and there it does
> the mpirun. This does not work with your settings (probably because you
> do not load the modules in your .bashrc (or .cshrc), but only in your
> slurm-job and your system does not transfer the environment with ssh.
>
> The recommended option for mpi version 2 (all modern mpis) is to set
> MPI_REMOTE to zero. The mpirun command will be issued on the original
> node, but the lapw1_mpi executables will run as given in .machines.
>
> This should solve your problem.
>
> Am 29.05.2021 um 08:39 schrieb leila mollabashi:
> > Dear all wien2k users,
> > Following the previous comment referring me to the admin, I contacted
> > the cluster admin. By the comment of the admin, I recompiled Wien2k
> > successfully using the cluster modules.
> >>Once the blacs problem has been fixed,
> > For example, is the following correct?
> > libmkl_blacs_openmpi_lp64.so =>
> >
> /opt/exp_soft/local/generic/intel/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so
>
> > (0x2b21efe03000)
> >>the next step is to run lapw0 in
> > sequential and parallel mode.
> >>Add:
> > x lapw0 and check the case.output0 and case.scf0 files (copy them to
> > a different name) as well as the message from the queuing system. ...
> > The “x lapw0” and “mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def” are
> > interactively executed correctly.
> > The “x lapw0 -p” is also correctly executed using the following
> > “.machines” file:
> > lapw0:e0017:4
> >>The same thing could be made with lapw1
> > The “x lapw1” and “mpirun -np 4 $WIENROOT/lapw1_mpi lapw1.def” are also
> > correctly executed interactively with no problem. But “x lapw1 -p” stops
> > when I use the following “.machines” file:
> > 1:e0017:2
> > 1:e0017:2
> > bash: mpirun: command not found
> > The output files are gathered into https://files.fm/u/7cssehdck
> > .
> > Would you, please, help me to fix the parallel problem too?
> > Sincerely yours,
> > Leila
> >
> >
> > ___
> > 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
> >
>
> --
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at
> -
> ___
> 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
>
___
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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] MPI Error

[leila mollabashi]

Dear all Wien2k users,
It is a pleasure to report that at last my problem is solved.
Here, I would like to express my gratitude to Peter Blaha, Laurence Marks,
Gavin Abo and Fecher Gerhard for all their very nice and valuable comments
and helpful links.
Sincerely yours,
Leila


On Sat, May 29, 2021 at 7:07 PM Peter Blaha 
wrote:

> The difference beteen lapw0para and lapw1para is that
> lapw0para always executes mpirun on the original node, lapw1para maybe not.
>
> The behavior of lapw1para depends on MPI_REMOTE (set in
> WIEN2k_parallel_options in w2k21.1 (or parallel_options earlier).
> With MPI_REMOTE=1 it will first issue a   ssh nodename and there it does
> the mpirun. This does not work with your settings (probably because you
> do not load the modules in your .bashrc (or .cshrc), but only in your
> slurm-job and your system does not transfer the environment with ssh.
>
> The recommended option for mpi version 2 (all modern mpis) is to set
> MPI_REMOTE to zero. The mpirun command will be issued on the original
> node, but the lapw1_mpi executables will run as given in .machines.
>
> This should solve your problem.
>
> Am 29.05.2021 um 08:39 schrieb leila mollabashi:
> > Dear all wien2k users,
> > Following the previous comment referring me to the admin, I contacted
> > the cluster admin. By the comment of the admin, I recompiled Wien2k
> > successfully using the cluster modules.
> >>Once the blacs problem has been fixed,
> > For example, is the following correct?
> > libmkl_blacs_openmpi_lp64.so =>
> >
> /opt/exp_soft/local/generic/intel/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so
>
> > (0x2b21efe03000)
> >>the next step is to run lapw0 in
> > sequential and parallel mode.
> >>Add:
> > x lapw0 and check the case.output0 and case.scf0 files (copy them to
> > a different name) as well as the message from the queuing system. ...
> > The “x lapw0” and “mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def” are
> > interactively executed correctly.
> > The “x lapw0 -p” is also correctly executed using the following
> > “.machines” file:
> > lapw0:e0017:4
> >>The same thing could be made with lapw1
> > The “x lapw1” and “mpirun -np 4 $WIENROOT/lapw1_mpi lapw1.def” are also
> > correctly executed interactively with no problem. But “x lapw1 -p” stops
> > when I use the following “.machines” file:
> > 1:e0017:2
> > 1:e0017:2
> > bash: mpirun: command not found
> > The output files are gathered into https://files.fm/u/7cssehdck
> > .
> > Would you, please, help me to fix the parallel problem too?
> > Sincerely yours,
> > Leila
> >
> >
> > ___
> > 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
> >
>
> --
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at
> -
> ___
> 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
>
___
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Re: [Wien] MPI Error

[Laurence Marks]

Confusius say "teach a woman to fish..."

Please read the pages I sent, and search for other ones.

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Sat, May 29, 2021, 09:37 Peter Blaha 
wrote:

> The difference beteen lapw0para and lapw1para is that
> lapw0para always executes mpirun on the original node, lapw1para maybe not.
>
> The behavior of lapw1para depends on MPI_REMOTE (set in
> WIEN2k_parallel_options in w2k21.1 (or parallel_options earlier).
> With MPI_REMOTE=1 it will first issue a   ssh nodename and there it does
> the mpirun. This does not work with your settings (probably because you
> do not load the modules in your .bashrc (or .cshrc), but only in your
> slurm-job and your system does not transfer the environment with ssh.
>
> The recommended option for mpi version 2 (all modern mpis) is to set
> MPI_REMOTE to zero. The mpirun command will be issued on the original
> node, but the lapw1_mpi executables will run as given in .machines.
>
> This should solve your problem.
>
> Am 29.05.2021 um 08:39 schrieb leila mollabashi:
> > Dear all wien2k users,
> > Following the previous comment referring me to the admin, I contacted
> > the cluster admin. By the comment of the admin, I recompiled Wien2k
> > successfully using the cluster modules.
> >>Once the blacs problem has been fixed,
> > For example, is the following correct?
> > libmkl_blacs_openmpi_lp64.so =>
> >
> /opt/exp_soft/local/generic/intel/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so
>
> > (0x2b21efe03000)
> >>the next step is to run lapw0 in
> > sequential and parallel mode.
> >>Add:
> > x lapw0 and check the case.output0 and case.scf0 files (copy them to
> > a different name) as well as the message from the queuing system. ...
> > The “x lapw0” and “mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def” are
> > interactively executed correctly.
> > The “x lapw0 -p” is also correctly executed using the following
> > “.machines” file:
> > lapw0:e0017:4
> >>The same thing could be made with lapw1
> > The “x lapw1” and “mpirun -np 4 $WIENROOT/lapw1_mpi lapw1.def” are also
> > correctly executed interactively with no problem. But “x lapw1 -p” stops
> > when I use the following “.machines” file:
> > 1:e0017:2
> > 1:e0017:2
> > bash: mpirun: command not found
> > The output files are gathered into
> https://urldefense.com/v3/__https://files.fm/u/7cssehdck__;!!Dq0X2DkFhyF93HkjWTBQKhk!GehhKM9_lavI3Z1GhfDhsFyx7zMc7VvOH3yKoeH7URNRlGfgGX4Q4IWmoSniXNxgBRiDKA$
>
> > <
> https://urldefense.com/v3/__https://files.fm/u/7cssehdck__;!!Dq0X2DkFhyF93HkjWTBQKhk!GehhKM9_lavI3Z1GhfDhsFyx7zMc7VvOH3yKoeH7URNRlGfgGX4Q4IWmoSniXNxgBRiDKA$
> >.
> > Would you, please, help me to fix the parallel problem too?
> > Sincerely yours,
> > Leila
> >
> >
> > ___
> > Wien mailing list
> > Wien@zeus.theochem.tuwien.ac.at
> >
> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!GehhKM9_lavI3Z1GhfDhsFyx7zMc7VvOH3yKoeH7URNRlGfgGX4Q4IWmoSniXNzoGi-Haw$
> > SEARCH the MAILING-LIST at:
> https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!GehhKM9_lavI3Z1GhfDhsFyx7zMc7VvOH3yKoeH7URNRlGfgGX4Q4IWmoSniXNyORHdTTQ$
> >
>
> --
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k:
> https://urldefense.com/v3/__http://www.wien2k.at__;!!Dq0X2DkFhyF93HkjWTBQKhk!GehhKM9_lavI3Z1GhfDhsFyx7zMc7VvOH3yKoeH7URNRlGfgGX4Q4IWmoSniXNxoY0Guuw$
> WWW:
> https://urldefense.com/v3/__http://www.imc.tuwien.ac.at__;!!Dq0X2DkFhyF93HkjWTBQKhk!GehhKM9_lavI3Z1GhfDhsFyx7zMc7VvOH3yKoeH7URNRlGfgGX4Q4IWmoSniXNwJDDxRHg$
> -
> ___
> Wien mailing list
> Wien@zeus.theochem.tuwien.ac.at
>
> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!GehhKM9_lavI3Z1GhfDhsFyx7zMc7VvOH3yKoeH7URNRlGfgGX4Q4IWmoSniXNzoGi-Haw$
> SEARCH the MAILING-LIST at:
> https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!GehhKM9_lavI3Z1GhfDhsFyx7zMc7VvOH3yKoeH7URNRlGfgGX4Q4IWmoSniXNyORHdTTQ$
>
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Re: [Wien] MPI Error

[Peter Blaha]

The difference beteen lapw0para and lapw1para is that
lapw0para always executes mpirun on the original node, lapw1para maybe not.

The behavior of lapw1para depends on MPI_REMOTE (set in 
WIEN2k_parallel_options in w2k21.1 (or parallel_options earlier).
With MPI_REMOTE=1 it will first issue a   ssh nodename and there it does 
the mpirun. This does not work with your settings (probably because you 
do not load the modules in your .bashrc (or .cshrc), but only in your 
slurm-job and your system does not transfer the environment with ssh.


The recommended option for mpi version 2 (all modern mpis) is to set 
MPI_REMOTE to zero. The mpirun command will be issued on the original 
node, but the lapw1_mpi executables will run as given in .machines.


This should solve your problem.

Am 29.05.2021 um 08:39 schrieb leila mollabashi:

Dear all wien2k users,
Following the previous comment referring me to the admin, I contacted 
the cluster admin. By the comment of the admin, I recompiled Wien2k 
successfully using the cluster modules.

Once the blacs problem has been fixed,

For example, is the following correct?
libmkl_blacs_openmpi_lp64.so => 
/opt/exp_soft/local/generic/intel/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so 
(0x2b21efe03000)

the next step is to run lapw0 in

sequential and parallel mode.

Add:

x lapw0     and check the case.output0 and case.scf0 files (copy them to
a different name) as well as the message from the queuing system. ...
The “x lapw0” and “mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def” are 
interactively executed correctly.
The “x lapw0 -p” is also correctly executed using the following 
“.machines” file:

lapw0:e0017:4

The same thing could be made with lapw1
The “x lapw1” and “mpirun -np 4 $WIENROOT/lapw1_mpi lapw1.def” are also 
correctly executed interactively with no problem. But “x lapw1 -p” stops 
when I use the following “.machines” file:

1:e0017:2
1:e0017:2
bash: mpirun: command not found
The output files are gathered into https://files.fm/u/7cssehdck 
.

Would you, please, help me to fix the parallel problem too?
Sincerely yours,
Leila


___
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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at
-
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Re: [Wien] MPI Error

[Laurence Marks]

As we have told you before, mpirun is a command on your system, it is not
part of Wien2k. Your problem is because you have something wrong in what is
defined (probably) for your PATH variable, and/or how this is exported --
my guess.

I suggest you read
http://www.linfo.org/path_env_var.html#:~:text=PATH%20is%20an%20environmental%20variable,commands%20issued%20by%20a%20user
.
https://www.javatpoint.com/linux-export-command
https://www.javatpoint.com/linux-tutorial

Reading is the best way to solve your problems. When you understand more
you will be able to fix things.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Sat, May 29, 2021, 01:40 leila mollabashi 
wrote:

> Dear all wien2k users,
> Following the previous comment referring me to the admin, I contacted the
> cluster admin. By the comment of the admin, I recompiled Wien2k
> successfully using the cluster modules.
> >Once the blacs problem has been fixed,
> For example, is the following correct?
> libmkl_blacs_openmpi_lp64.so =>
> /opt/exp_soft/local/generic/intel/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so
> (0x2b21efe03000)
> >the next step is to run lapw0 in
> sequential and parallel mode.
> >Add:
> x lapw0 and check the case.output0 and case.scf0 files (copy them to
> a different name) as well as the message from the queuing system. ...
> The “x lapw0” and “mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def” are
> interactively executed correctly.
> The “x lapw0 -p” is also correctly executed using the following
> “.machines” file:
> lapw0:e0017:4
> >The same thing could be made with lapw1
> The “x lapw1” and “mpirun -np 4 $WIENROOT/lapw1_mpi lapw1.def” are also
> correctly executed interactively with no problem. But “x lapw1 -p” stops
> when I use the following “.machines” file:
> 1:e0017:2
> 1:e0017:2
> bash: mpirun: command not found
> The output files are gathered into https://files.fm/u/7cssehdck
> .
>
> Would you, please, help me to fix the parallel problem too?
> Sincerely yours,
> Leila
>
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Re: [Wien] MPI error

[Peter Blaha]

As Laurence Marks mentioned, looking into all files you proposed, would 
cost a couple of hours. You have to check these files yourself and solve 
the problem or at least extract the most important information.



A few remarks:

  > You need to link with the blacs library for openmpi.
I unsuccessfully recompiled wien2k by linking with the blacs library
for openmpias “mkl_blacs_openmpi_lp64” due to gfortran errors. 


The compile messages show that the serial version was compiled with 
ifort (and also the compiler options are for ifort). For mpi you used 
mpif90, however, this links to gfortran. Your compiler options for ifort 
are of course not compatible with this.
You need a different mpi-compiler, which links to ifort (maybe mpifort, 
this is what we have for our openmpi+ifort installation (with one i 
only!!) I would retry the installation but with mpifort as mpi-compiler)



The openmpi and fftw of the cluster are compiled with gfortran. So I
have also installed openmpi 4.1.0 and fftw3.3.9 in my home directory
after loading ifort and icc with the following commands:


Compilation looks ok, but:
your own openmpi is configured only for Gbit ethernet, not for 
Infiniband (please "read" the error message). If you really want to use 
your own openmpi, it needs to be configured for Infiniband.


In any case, a "good" supercomputer system should have "compatible" 
modules and you have to select the proper modules, which work together.


I'm pretty sure that everything is there what you need, but it looks 
that none of the sys-admins can really help or knows the details, 
how/which modules one should use and which commands one should use.



./configure--prefix=/home/users/mollabashi/expands/openmpi CC=icc
F77=ifort FC=ifort--with-slurm --with-pmix --enable-shared
--with-hwloc=internal
./configure--prefix=/home/users/mollabashi/expands/fftw MPICC=mpicc
CC=icc F77=ifort --enable-mpi --enable-openmp  --enable-shared
By this way, Wien2k compiled correctly as shown in the video in
_https://files.fm/u/rk3vfqv5g

_
link. But mpi run does not run due to the error about openmpi as in:
_https://files.fm/u/tcz2fvwpg

_.
The .bashrc, submit.sh and slurm.out filesare in
_https://files.fm/u/dnrrwqguy

_
link.
Would you please guide me how to solve the gfortran errors?
Should I install openmpi with another configuration to solve the
slurm error of mpi calculation?
Sincerely yours,
Leila


--
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 
"Research is to see what everybody else has seen, and to think what 
nobody else has thought" Albert Szent-Györgyi


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--
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at
-
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Re: [Wien] MPI error

[Laurence Marks]

You MUST read your files yourself FIRST, and use some logic.

The files for lapw0/lapw1 you include indicate that you used ifort/icc for
the non-parallel parts. However, the parallel parts uses mpif90 which on
your system points to gfortran. You need to use the parallel version of
ifort, which is probably mpiifort (and mpiic), but may not be. You have to
look.

I do not know if that is your problem because your email is long and
confusing (perhaps confused). Please keep it simple (KISS). mpif90

On Wed, May 19, 2021 at 2:13 PM leila mollabashi 
wrote:

> Dear all wien2k users,
> Thankyou for your reply and guides.
>  > You need to link with the blacs library for openmpi.
> I unsuccessfully recompiled wien2k by linking with the blacs library for
> openmpias “mkl_blacs_openmpi_lp64” due to gfortran errors. The video of
> this recompile is uploaded to a website which is available from: 
> *https://files.fm/u/zzwhjjj5q
> *
> link. The SRC_lapw0/lapw1 compile.msg files are uploaded to: 
> *https://files.fm/u/zuwukxy8x
> *
> ,* https://files.fm/u/cep4pvnvd
> *
> .
> The openmpi and fftw of the cluster are compiled with gfortran. So I have
> also installed openmpi 4.1.0 and fftw3.3.9 in my home directory after
> loading ifort and icc with the following commands:
> ./configure--prefix=/home/users/mollabashi/expands/openmpi CC=icc
> F77=ifort FC=ifort--with-slurm --with-pmix --enable-shared
> --with-hwloc=internal
> ./configure--prefix=/home/users/mollabashi/expands/fftw MPICC=mpicc CC=icc
> F77=ifort --enable-mpi --enable-openmp  --enable-shared
> By this way, Wien2k compiled correctly as shown in the video in 
> *https://files.fm/u/rk3vfqv5g
> *
> link. But mpi run does not run due to the error about openmpi as in: 
> *https://files.fm/u/tcz2fvwpg
> *.
> The .bashrc, submit.sh and slurm.out filesare in *https://files.fm/u/dnrrwqguy
> *
> link.
> Would you please guide me how to solve the gfortran errors?
> Should I install openmpi with another configuration to solve the slurm
> error of mpi calculation?
> Sincerely yours,
> Leila
>

-- 
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody
else has thought" Albert Szent-Györgyi
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Re: [Wien] MPI error

[leila mollabashi]

Dear all wien2k users,
Thankyou for your reply and guides.
 > You need to link with the blacs library for openmpi.
I unsuccessfully recompiled wien2k by linking with the blacs library for
openmpias “mkl_blacs_openmpi_lp64” due to gfortran errors. The video of
this recompile is uploaded to a website which is available from:
*https://files.fm/u/zzwhjjj5q
* link. The SRC_lapw0/lapw1 compile.msg files
are uploaded to: *https://files.fm/u/zuwukxy8x
*,* https://files.fm/u/cep4pvnvd
*.
The openmpi and fftw of the cluster are compiled with gfortran. So I have
also installed openmpi 4.1.0 and fftw3.3.9 in my home directory after
loading ifort and icc with the following commands:
./configure--prefix=/home/users/mollabashi/expands/openmpi CC=icc F77=ifort
FC=ifort--with-slurm --with-pmix --enable-shared --with-hwloc=internal
./configure--prefix=/home/users/mollabashi/expands/fftw MPICC=mpicc CC=icc
F77=ifort --enable-mpi --enable-openmp  --enable-shared
By this way, Wien2k compiled correctly as shown in the video in
*https://files.fm/u/rk3vfqv5g
* link. But mpi run does not run due to the
error about openmpi as in: *https://files.fm/u/tcz2fvwpg
*. The .bashrc, submit.sh and slurm.out
filesare in *https://files.fm/u/dnrrwqguy *
link.
Would you please guide me how to solve the gfortran errors?
Should I install openmpi with another configuration to solve the slurm
error of mpi calculation?
Sincerely yours,
Leila

On Thu, May 6, 2021 at 9:44 PM Laurence Marks 
wrote:

> Peter beat me to the response -- please do as he says and move stepwise
> forward, posting single steps if they fail.
>
> On Thu, May 6, 2021 at 10:38 AM Peter Blaha 
> wrote:
>
>> Once the blacs problem has been fixed, the next step is to run lapw0 in
>> sequential and parallel mode.
>>
>> Add:
>>
>> x lapw0 and check the case.output0 and case.scf0 files (copy them to
>> a different name) as well as the message from the queuing system.
>>
>> add:   mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def
>> and check the messages and compare the results with the previous
>> sequential run.
>>
>> And finally:
>> create a .machines file with:
>> lapw0:localhost:4
>>
>> and execute
>> x lapw0 -p
>>
>> -
>> The same thing could be made with lapw1
>>
>>
>> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought" Albert Szent-Györgyi
> ___
> Wien mailing list
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> 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
>
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Re: [Wien] MPI error

[Laurence Marks]

Peter beat me to the response -- please do as he says and move stepwise
forward, posting single steps if they fail.

On Thu, May 6, 2021 at 10:38 AM Peter Blaha 
wrote:

> Once the blacs problem has been fixed, the next step is to run lapw0 in
> sequential and parallel mode.
>
> Add:
>
> x lapw0 and check the case.output0 and case.scf0 files (copy them to
> a different name) as well as the message from the queuing system.
>
> add:   mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def
> and check the messages and compare the results with the previous
> sequential run.
>
> And finally:
> create a .machines file with:
> lapw0:localhost:4
>
> and execute
> x lapw0 -p
>
> -
> The same thing could be made with lapw1
>
>
> --
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody
else has thought" Albert Szent-Györgyi
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Re: [Wien] MPI error

[Peter Blaha]

Once the blacs problem has been fixed, the next step is to run lapw0 in 
sequential and parallel mode.


Add:

x lapw0 and check the case.output0 and case.scf0 files (copy them to 
a different name) as well as the message from the queuing system.


add:   mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def
and check the messages and compare the results with the previous 
sequential run.


And finally:
create a .machines file with:
lapw0:localhost:4

and execute
x lapw0 -p

-
The same thing could be made with lapw1

Am 06.05.2021 um 15:09 schrieb leila mollabashi:

Dear all wien2k users,
 >I suggest that you focus on the PATH first, using
I followed your suggestion. The script and results are in the 
https://files.fm/u/m2qak574g . The 
compile.msg_lapw0 and compile.msg_lapw0 are in the 
https://files.fm/u/pvdn52zpw  .


Sincerely yours,

Leila


On Wed, May 5, 2021 at 5:14 PM Laurence Marks > wrote:


I think we (collectively) may be confusing things by offering too
much advice!

Let's keep it simple, and focus on one thing at a time. The "mpirun
not found" has nothing to do with compilers. It is 100% due to your
not having the PATH variable set right. This is not fftw, but
probably in the general options and mpi module. (It is not in the
compiler.)

The library not being found is similarly due to LD_LIBRARY_PATH not
being right, or perhaps nfs mounting issues. This may be from the
compiler variables (mpiifort for Intel), which may not be correctly
set by the module.

I suggest that you focus on the PATH first, using
which mpirun
which lapw1
echo $PATH
echo $WIENROOT

When this is correct in the script that runs your job we can move
forward and solve the library issue using
echo $LD_LIBRARY_PATH
ldd $WIENROOT/lapw1_mpi
ldd $WIENROOT/lapw0_mpi

Please focus just of the PATH first. If you have problems, find a
way (DropBox/Drive etc) to post the script and result.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what
nobody else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu 

On Tue, May 4, 2021, 22:24 Gavin Abo mailto:gs...@crimson.ua.edu>> wrote:

Three additional comments:

1)  If you are running the slurm.job script as Non-Interactive
[1,2], you might need a "source /etc/profile.d/ummodules.csh"
line like that at [3].

[1] https://slurm.schedmd.com/faq.html#sbatch_srun


[2]
https://wiki.umiacs.umd.edu/umiacs/index.php/SLURM/JobSubmission


[3] https://wiki.umiacs.umd.edu/umiacs/index.php/Modules



2) To eliminate any possible conflicts between Intel compilers
(ifort, icc) and GNU compilers (gfortran, gcc) such as those
mentioned in posts [4,5].  I suggest compiling of WIEN2k using
the same C compiler and Fortran compiler that Open MPI was
compiled with.

The commands [6] below might help you check that the Linux
environment is using the intended Open MPI and mpi parallel
compilers [7]:

username@computername:~/Desktop$ mpirun -V
mpirun (Open MPI) 4.1.1

Report bugs to http://www.open-mpi.org/community/help/


username@computername:~/Desktop$ mpicc --showme:version
mpicc: Open MPI 4.1.1 (Language: C)
username@computername:~/Desktop$ mpifort --showme:version
mpifort: Open MPI 4.1.1 (Language: Fortran)
username@computername:~/Desktop$ mpicc --version
gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

username@computername:~/Desktop$ mpifort --version
GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying 

Re: [Wien] MPI error

[Peter Blaha]

One thing is clear:

lapw1_mpi cannot work.

You are linking with-lmkl_blacs_intelmpi_lp64

but you are using openmpi.

You need to link with the blacs library for openmpi.

It is mentioned in the usersguide.

Am 06.05.2021 um 15:09 schrieb leila mollabashi:

Dear all wien2k users,
 >I suggest that you focus on the PATH first, using
I followed your suggestion. The script and results are in the 
https://files.fm/u/m2qak574g . The 
compile.msg_lapw0 and compile.msg_lapw0 are in the 
https://files.fm/u/pvdn52zpw  .


Sincerely yours,

Leila


On Wed, May 5, 2021 at 5:14 PM Laurence Marks > wrote:


I think we (collectively) may be confusing things by offering too
much advice!

Let's keep it simple, and focus on one thing at a time. The "mpirun
not found" has nothing to do with compilers. It is 100% due to your
not having the PATH variable set right. This is not fftw, but
probably in the general options and mpi module. (It is not in the
compiler.)

The library not being found is similarly due to LD_LIBRARY_PATH not
being right, or perhaps nfs mounting issues. This may be from the
compiler variables (mpiifort for Intel), which may not be correctly
set by the module.

I suggest that you focus on the PATH first, using
which mpirun
which lapw1
echo $PATH
echo $WIENROOT

When this is correct in the script that runs your job we can move
forward and solve the library issue using
echo $LD_LIBRARY_PATH
ldd $WIENROOT/lapw1_mpi
ldd $WIENROOT/lapw0_mpi

Please focus just of the PATH first. If you have problems, find a
way (DropBox/Drive etc) to post the script and result.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what
nobody else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu 

On Tue, May 4, 2021, 22:24 Gavin Abo mailto:gs...@crimson.ua.edu>> wrote:

Three additional comments:

1)  If you are running the slurm.job script as Non-Interactive
[1,2], you might need a "source /etc/profile.d/ummodules.csh"
line like that at [3].

[1] https://slurm.schedmd.com/faq.html#sbatch_srun


[2]
https://wiki.umiacs.umd.edu/umiacs/index.php/SLURM/JobSubmission


[3] https://wiki.umiacs.umd.edu/umiacs/index.php/Modules



2) To eliminate any possible conflicts between Intel compilers
(ifort, icc) and GNU compilers (gfortran, gcc) such as those
mentioned in posts [4,5].  I suggest compiling of WIEN2k using
the same C compiler and Fortran compiler that Open MPI was
compiled with.

The commands [6] below might help you check that the Linux
environment is using the intended Open MPI and mpi parallel
compilers [7]:

username@computername:~/Desktop$ mpirun -V
mpirun (Open MPI) 4.1.1

Report bugs to http://www.open-mpi.org/community/help/


username@computername:~/Desktop$ mpicc --showme:version
mpicc: Open MPI 4.1.1 (Language: C)
username@computername:~/Desktop$ mpifort --showme:version
mpifort: Open MPI 4.1.1 (Language: Fortran)
username@computername:~/Desktop$ mpicc --version
gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

username@computername:~/Desktop$ mpifort --version
GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

[4]

https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08315.html

Re: [Wien] MPI error

[leila mollabashi]

Dear all wien2k users,
>I suggest that you focus on the PATH first, using
I followed your suggestion. The script and results are in the
https://files.fm/u/m2qak574g. The compile.msg_lapw0 and  compile.msg_lapw0
are in the  https://files.fm/u/pvdn52zpw .

Sincerely yours,

Leila


On Wed, May 5, 2021 at 5:14 PM Laurence Marks 
wrote:

> I think we (collectively) may be confusing things by offering too much
> advice!
>
> Let's keep it simple, and focus on one thing at a time. The "mpirun not
> found" has nothing to do with compilers. It is 100% due to your not having
> the PATH variable set right. This is not fftw, but probably in the general
> options and mpi module. (It is not in the compiler.)
>
> The library not being found is similarly due to LD_LIBRARY_PATH not being
> right, or perhaps nfs mounting issues. This may be from the compiler
> variables (mpiifort for Intel), which may not be correctly set by the
> module.
>
> I suggest that you focus on the PATH first, using
> which mpirun
> which lapw1
> echo $PATH
> echo $WIENROOT
>
> When this is correct in the script that runs your job we can move forward
> and solve the library issue using
> echo $LD_LIBRARY_PATH
> ldd $WIENROOT/lapw1_mpi
> ldd $WIENROOT/lapw0_mpi
>
> Please focus just of the PATH first. If you have problems, find a way
> (DropBox/Drive etc) to post the script and result.
>
> _
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu
>
> On Tue, May 4, 2021, 22:24 Gavin Abo  wrote:
>
>> Three additional comments:
>>
>> 1)  If you are running the slurm.job script as Non-Interactive [1,2], you
>> might need a "source /etc/profile.d/ummodules.csh" line like that at [3].
>> [1] https://slurm.schedmd.com/faq.html#sbatch_srun
>> 
>> [2] https://wiki.umiacs.umd.edu/umiacs/index.php/SLURM/JobSubmission
>> 
>> [3] https://wiki.umiacs.umd.edu/umiacs/index.php/Modules
>> 
>>
>> 2) To eliminate any possible conflicts between Intel compilers (ifort,
>> icc) and GNU compilers (gfortran, gcc) such as those mentioned in posts
>> [4,5].  I suggest compiling of WIEN2k using the same C compiler and Fortran
>> compiler that Open MPI was compiled with.
>>
>> The commands [6] below might help you check that the Linux environment is
>> using the intended Open MPI and mpi parallel compilers [7]:
>>
>> username@computername:~/Desktop$ mpirun -V
>> mpirun (Open MPI) 4.1.1
>>
>> Report bugs to http://www.open-mpi.org/community/help/
>> 
>> username@computername:~/Desktop$ mpicc --showme:version
>> mpicc: Open MPI 4.1.1 (Language: C)
>> username@computername:~/Desktop$ mpifort --showme:version
>> mpifort: Open MPI 4.1.1 (Language: Fortran)
>> username@computername:~/Desktop$ mpicc --version
>> gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
>> Copyright (C) 2019 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.  There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>> PURPOSE.
>>
>> username@computername:~/Desktop$ mpifort --version
>> GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
>> Copyright (C) 2019 Free Software Foundation, Inc.
>> This is free software; see the source for copying conditions.  There is NO
>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
>> PURPOSE.
>> [4]
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08315.html
>> 
>> [5]
>> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17052.html
>> 
>> [6]
>> https://stackoverflow.com/questions/10056898/how-do-you-check-the-version-of-openmpi
>> 

Re: [Wien] MPI error

[Laurence Marks]

I think we (collectively) may be confusing things by offering too much
advice!

Let's keep it simple, and focus on one thing at a time. The "mpirun not
found" has nothing to do with compilers. It is 100% due to your not having
the PATH variable set right. This is not fftw, but probably in the general
options and mpi module. (It is not in the compiler.)

The library not being found is similarly due to LD_LIBRARY_PATH not being
right, or perhaps nfs mounting issues. This may be from the compiler
variables (mpiifort for Intel), which may not be correctly set by the
module.

I suggest that you focus on the PATH first, using
which mpirun
which lapw1
echo $PATH
echo $WIENROOT

When this is correct in the script that runs your job we can move forward
and solve the library issue using
echo $LD_LIBRARY_PATH
ldd $WIENROOT/lapw1_mpi
ldd $WIENROOT/lapw0_mpi

Please focus just of the PATH first. If you have problems, find a way
(DropBox/Drive etc) to post the script and result.

_
Professor Laurence Marks
"Research is to see what everybody else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Tue, May 4, 2021, 22:24 Gavin Abo  wrote:

> Three additional comments:
>
> 1)  If you are running the slurm.job script as Non-Interactive [1,2], you
> might need a "source /etc/profile.d/ummodules.csh" line like that at [3].
> [1] https://slurm.schedmd.com/faq.html#sbatch_srun
> 
> [2] https://wiki.umiacs.umd.edu/umiacs/index.php/SLURM/JobSubmission
> 
> [3] https://wiki.umiacs.umd.edu/umiacs/index.php/Modules
> 
>
> 2) To eliminate any possible conflicts between Intel compilers (ifort,
> icc) and GNU compilers (gfortran, gcc) such as those mentioned in posts
> [4,5].  I suggest compiling of WIEN2k using the same C compiler and Fortran
> compiler that Open MPI was compiled with.
>
> The commands [6] below might help you check that the Linux environment is
> using the intended Open MPI and mpi parallel compilers [7]:
>
> username@computername:~/Desktop$ mpirun -V
> mpirun (Open MPI) 4.1.1
>
> Report bugs to http://www.open-mpi.org/community/help/
> 
> username@computername:~/Desktop$ mpicc --showme:version
> mpicc: Open MPI 4.1.1 (Language: C)
> username@computername:~/Desktop$ mpifort --showme:version
> mpifort: Open MPI 4.1.1 (Language: Fortran)
> username@computername:~/Desktop$ mpicc --version
> gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
> Copyright (C) 2019 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> username@computername:~/Desktop$ mpifort --version
> GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
> Copyright (C) 2019 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> [4]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08315.html
> 
> [5]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17052.html
> 
> [6]
> https://stackoverflow.com/questions/10056898/how-do-you-check-the-version-of-openmpi
> 
> [7] https://www.open-mpi.org/faq/?category=mpi-apps#general-build
> 
>
> 3) Those cluster administrators are usually more savvy than I am with
> installation and optimization of software (using compiler documentation,
> e.g. [8,9]) on a high 

Re: [Wien] MPI error

[Gavin Abo]

Three additional comments:

1)  If you are running the slurm.job script as Non-Interactive [1,2], 
you might need a "source /etc/profile.d/ummodules.csh" line like that at 
[3].


[1] https://slurm.schedmd.com/faq.html#sbatch_srun
[2] https://wiki.umiacs.umd.edu/umiacs/index.php/SLURM/JobSubmission
[3] https://wiki.umiacs.umd.edu/umiacs/index.php/Modules

2) To eliminate any possible conflicts between Intel compilers (ifort, 
icc) and GNU compilers (gfortran, gcc) such as those mentioned in posts 
[4,5].  I suggest compiling of WIEN2k using the same C compiler and 
Fortran compiler that Open MPI was compiled with.


The commands [6] below might help you check that the Linux environment 
is using the intended Open MPI and mpi parallel compilers [7]:


username@computername:~/Desktop$ mpirun -V
mpirun (Open MPI) 4.1.1

Report bugs to http://www.open-mpi.org/community/help/
username@computername:~/Desktop$ mpicc --showme:version
mpicc: Open MPI 4.1.1 (Language: C)
username@computername:~/Desktop$ mpifort --showme:version
mpifort: Open MPI 4.1.1 (Language: Fortran)
username@computername:~/Desktop$ mpicc --version
gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

username@computername:~/Desktop$ mpifort --version
GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[4] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08315.html
[5] 
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17052.html
[6] 
https://stackoverflow.com/questions/10056898/how-do-you-check-the-version-of-openmpi

[7] https://www.open-mpi.org/faq/?category=mpi-apps#general-build

3) Those cluster administrators are usually more savvy than I am with 
installation and optimization of software (using compiler documentation, 
e.g. [8,9]) on a high performance computing (hpc) supercomputer 
[10,11].  They would know your situation better. For example, they could 
login to their administrator account on the cluster to install WIEN2k 
only in your user account directory (/home/users/mollabashi), and they 
would know how to set the appropriate access permissions [12].  
Alternatively, if your not using a personal laptop but a computer at the 
organization to remotely connect to the cluster then they might use 
remote desktop access [13] to help you with the installation within only 
your account.  Or they might use another method.


[8] 
https://software.intel.com/content/www/us/en/develop/articles/download-documentation-intel-compiler-current-and-previous.html

[9] https://gcc.gnu.org/onlinedocs/
[10] 
https://www.usgs.gov/core-science-systems/sas/arc/about/what-high-performance-computing

[11] https://en.wikipedia.org/wiki/Supercomputer
[12] 
https://www.oreilly.com/library/view/running-linux-third/156592469X/ch04s14.html

[13] https://en.wikipedia.org/wiki/Desktop_sharing

On 5/4/2021 3:40 PM, Laurence Marks wrote:
For certain, 
"/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec 
/home/users/mollabashi/codes/v21.1/run_lapw -p" is completely wrong. 
You do not, repear do not use mpirun or mpiexec to start run_lapw. It 
has to be started by simply "run_lapw -p ..." by itself.


I suggest that you create a very simple job which has the commands:

which mpirun
which lapw1_mpi
echo $WIENROOT
ldd $WIENROOT/lapw1_mpi
ldd $WIENROOT/lapw1
echo env
echo $PATH

Run this interactively as well as in a batch job and compare. You will 
find that there are something which are not present when you are 
launching your slurm job that are present interactively. You need to 
repair these with relevant PATH/LD_LIBRARY_PATH etc


Your problems are not Wien2k problems, they are due to incorrect 
modules/script/environment or similar. Have you asked your sysadmin 
for help? I am certain that someone local who is experienced with 
standard linux can tell you very quickly what to do.


N.B., there is an error in your path setting.

On Tue, May 4, 2021 at 3:38 PM leila mollabashi 
mailto:le.mollaba...@gmail.com>> wrote:


Dear all WIEN2k users,
Thank you for your guides.
>take care on the correct location ...
It is the /usr/share/Modules/init
After adding the “source /usr/share/Modules/init/tcsh” line in to
the script the same error appeared:
mpirun: command not found

In fact, with and without “source /usr/share/Modules/init/tcsh” it
is written in slurm.out file that “ module load complete ”.

I noticed that “export” is also the bash command so I used these
commands to path the openmpi and fftw:
setenv LD_LIBRARY_PATH

Re: [Wien] MPI error

[Laurence Marks]

For certain, "/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec
/home/users/mollabashi/codes/v21.1/run_lapw -p" is completely wrong. You do
not, repear do not use mpirun or mpiexec to start run_lapw. It has to be
started by simply "run_lapw -p ..." by itself.

I suggest that you create a very simple job which has the commands:

which mpirun
which lapw1_mpi
echo $WIENROOT
ldd $WIENROOT/lapw1_mpi
ldd $WIENROOT/lapw1
echo env
echo $PATH

Run this interactively as well as in a batch job and compare. You will find
that there are something which are not present when you are launching your
slurm job that are present interactively. You need to repair these with
relevant PATH/LD_LIBRARY_PATH etc

Your problems are not Wien2k problems, they are due to incorrect
modules/script/environment or similar. Have you asked your sysadmin for
help? I am certain that someone local who is experienced with standard
linux can tell you very quickly what to do.

N.B., there is an error in your path setting.

On Tue, May 4, 2021 at 3:38 PM leila mollabashi 
wrote:

> Dear all WIEN2k users,
> Thank you for your guides.
> >take care on the correct location ...
> It is the /usr/share/Modules/init
> After adding the “source /usr/share/Modules/init/tcsh” line in to the
> script the same error appeared:
> mpirun: command not found
>
> In fact, with and without “source /usr/share/Modules/init/tcsh” it is
> written in slurm.out file that “ module load complete ”.
>
> I noticed that “export” is also the bash command so I used these commands
> to path the openmpi and fftw:
> setenv LD_LIBRARY_PATH
> {$LD_LIBRARY_PATH}:/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib
> set path = ($path
> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin)
> But result is the same:
> bash: mpirun: command not found
>
> By using this line in the script:
> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec
> /home/users/mollabashi/codes/v21.1/run_lapw -p
> The calculation stopped with the following error:
> mpirun does not support recursive calls
>
> > I wonder that you have only single modules…
> There are different versions of ifort and mkl: ifort/15.0.0, ifort/15.0.3,
> ifort/17.0.1, ifort/19.1.3.304(default) mkl/11.2, mkl/11.2.3.187
> 
>  mkl/2017.1.132,
> mkl/2019.2.187, mkl/2020.0.4(default). I used the defaults
> > you may also wish to make a single module file to be loaded…
> That is a good idea.
> > On our cluster we have different W2k modules ….
> As you know WIEN2k is not a free code and the users of the cluster that I
> am using are not registered WIEN2k users. Thus, according to my moral
> commitment to the WIEN2k developers, I cannot ask the administrator to
> install it on the cluster. I should install it on my user account.
>
> Sincerely yours,
> Leila
> >PS.: maybe one should mention this tcsh "problem" in the slurm.job
> example on the FAQ page by adding (or similar)…
> That is a good idea. Thank you for your suggestion.
>
> --
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu
"Research is to see what everybody else has seen, and to think what nobody
else has thought" Albert Szent-Györgyi
___
Wien mailing list
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SEARCH the MAILING-LIST at:  
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

Re: [Wien] MPI error

[leila mollabashi]

Dear all WIEN2k users,
Thank you for your guides.
>take care on the correct location ...
It is the /usr/share/Modules/init
After adding the “source /usr/share/Modules/init/tcsh” line in to the
script the same error appeared:
mpirun: command not found

In fact, with and without “source /usr/share/Modules/init/tcsh” it is
written in slurm.out file that “ module load complete ”.

I noticed that “export” is also the bash command so I used these commands
to path the openmpi and fftw:
setenv LD_LIBRARY_PATH
{$LD_LIBRARY_PATH}:/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib
set path = ($path
/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin)
But result is the same:
bash: mpirun: command not found

By using this line in the script:
/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec
/home/users/mollabashi/codes/v21.1/run_lapw -p
The calculation stopped with the following error:
mpirun does not support recursive calls

> I wonder that you have only single modules…
There are different versions of ifort and mkl: ifort/15.0.0, ifort/15.0.3,
ifort/17.0.1, ifort/19.1.3.304(default) mkl/11.2, mkl/11.2.3.187
mkl/2017.1.132,
mkl/2019.2.187, mkl/2020.0.4(default). I used the defaults
> you may also wish to make a single module file to be loaded…
That is a good idea.
> On our cluster we have different W2k modules ….
As you know WIEN2k is not a free code and the users of the cluster that I
am using are not registered WIEN2k users. Thus, according to my moral
commitment to the WIEN2k developers, I cannot ask the administrator to
install it on the cluster. I should install it on my user account.

Sincerely yours,
Leila
>PS.: maybe one should mention this tcsh "problem" in the slurm.job example
on the FAQ page by adding (or similar)…
That is a good idea. Thank you for your suggestion.

On Mon, May 3, 2021 at 4:18 PM Fecher, Gerhard  wrote:

> Dear Leila
> In your first mail you mentioned that you use
>  slurm.job
> with the added lines
>module load openmpi/4.1.0_gcc620
>module load ifort
>module load mkl
>
> Sorry that my Sunday evening answer was too short, here a little more
> detail:
> I guess your login shell is bash, and you run the command
>  sbatch slurm.job
> that is written for tcsh, but tcsh does not know where the module command
> is, therfore  the job file should tell it where it is,
> e.g.: the beginning of slurm.job should look like
>
> #!/bin/tcsh
> #
> # Load the respective software module you intend to use, here for tcsh
> shell
> # NOTE: you may need to edit the source line !
> source /usr/share/lmod/lmod/init/tcsh
> module load openmpi/4.1.0_gcc620
> module load ifort
> module load mkl
>
> take care on the correct location it may be in: /usr/share/modules/init/csh
> if you do not find its correct location then ask your administrator
>
> I wonder that you have only single modules for ifort and mkl and not
> different version,
> I guess that are defaults, but which ? ask your administrator;
> you may also wish to make a single module file to be loaded, and
> you may also whish to send the output to the data nirvana by using >&
> /dev/null
> in that case you may have only the lines (as an example)
> source /usr/share/lmod/lmod/init/tcsh
> module load Wien2k/wien2k_21_intel19 >& /dev/null
> echo -n "Running Wien2k" $WienVersion
>
>
> PS.: maybe one should mention this tcsh "problem"  in the slurm.job
> example on the FAQ page by adding (or similar)
>   #  NOTE: you may need to edit the following line !
>   #  source /usr/share/lmod/lmod/init/tcsh
> as modules are frequently used on clusters and allow easily to change
> between different versions.
> On our cluster we have different W2k modules that have been compiled with
> different libraries, compilers, and/or settings.
>
> PSS.: I am not aware of typos ;-)
>
> Ciao
> Gerhard
>
> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> "I think the problem, to be quite honest with you,
> is that you have never actually known what the question is."
>
> 
> Dr. Gerhard H. Fecher
> Institut of Physics
> Johannes Gutenberg - University
> 55099 Mainz
> 
> Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von leila
> mollabashi [le.mollaba...@gmail.com]
> Gesendet: Montag, 3. Mai 2021 00:35
> An: A Mailing list for WIEN2k users
> Betreff: Re: [Wien] MPI error
>
> Thank you.
>
> On Mon, May 3, 2021, 3:04 AM Laurence Marks  <mailto:laurence.ma...@gmail.com>> wrote:
> You have to solve the "mpirun not found". That is due to your
>

Re: [Wien] MPI error

[Fecher, Gerhard]

Dear Leila
In your first mail you mentioned that you use
 slurm.job
with the added lines 
   module load openmpi/4.1.0_gcc620
   module load ifort
   module load mkl

Sorry that my Sunday evening answer was too short, here a little more detail:
I guess your login shell is bash, and you run the command 
 sbatch slurm.job 
that is written for tcsh, but tcsh does not know where the module command is, 
therfore  the job file should tell it where it is, 
e.g.: the beginning of slurm.job should look like 

#!/bin/tcsh
#
# Load the respective software module you intend to use, here for tcsh shell
# NOTE: you may need to edit the source line !
source /usr/share/lmod/lmod/init/tcsh
module load openmpi/4.1.0_gcc620
module load ifort
module load mkl 

take care on the correct location it may be in: /usr/share/modules/init/csh
if you do not find its correct location then ask your administrator

I wonder that you have only single modules for ifort and mkl and not different 
version, 
I guess that are defaults, but which ? ask your administrator;
you may also wish to make a single module file to be loaded, and
you may also whish to send the output to the data nirvana by using >& /dev/null
in that case you may have only the lines (as an example)
source /usr/share/lmod/lmod/init/tcsh
module load Wien2k/wien2k_21_intel19 >& /dev/null
echo -n "Running Wien2k" $WienVersion


PS.: maybe one should mention this tcsh "problem"  in the slurm.job example on 
the FAQ page by adding (or similar)
  #  NOTE: you may need to edit the following line !
  #  source /usr/share/lmod/lmod/init/tcsh
as modules are frequently used on clusters and allow easily to change between 
different versions.
On our cluster we have different W2k modules that have been compiled with 
different libraries, compilers, and/or settings.

PSS.: I am not aware of typos ;-)

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Physics
Johannes Gutenberg - University
55099 Mainz

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von leila 
mollabashi [le.mollaba...@gmail.com]
Gesendet: Montag, 3. Mai 2021 00:35
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] MPI error

Thank you.

On Mon, May 3, 2021, 3:04 AM Laurence Marks 
mailto:laurence.ma...@gmail.com>> wrote:
You have to solve the "mpirun not found". That is due to your path/nfs/module 
-- we do not know.

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody else 
has thought", Albert Szent-Györgyi
www.numis.northwestern.edu<http://www.numis.northwestern.edu>

On Sun, May 2, 2021, 17:12 leila mollabashi 
mailto:le.mollaba...@gmail.com>> wrote:
>You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be 
>"...:$LD_LIB..."
Thank you. I have corrected it but I still have error in x lapw1 “mpirun: 
command not found”
>Why not load the modules in the script to run a job? I have loaded but this 
>error happened “bash: mpirun: command not found”.

On Mon, May 3, 2021 at 2:23 AM Laurence Marks 
mailto:laurence.ma...@gmail.com>> wrote:
You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be 
"...:$LD_LIB...".

Why not load the modules in the script to run a job?

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody else 
has thought", Albert Szent-Györgyi
www.numis.northwestern.edu<http://www.numis.northwestern.edu>

On Sun, May 2, 2021, 16:35 leila mollabashi 
mailto:le.mollaba...@gmail.com>> wrote:
Dear all WIEN2k users,
Thank you for your reply.
>The error is exactly what it says -- mpirun not found. This has something to 
>do with the modules, almost certainly the openmpi one. You need to find where 
>mpirun is on your system, and ensure that it is in your PATH. This is an issue 
>with your OS, not Wien2k. However...
which mpirun:
/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun
I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620,  
fftw/3.3.8_gcc620 modules. when I added the path in my .bashrc file as followes:
export 
LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH
export 
PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH
wien2k does not run:
error while loading shared libraries: libiomp5.so: cannot open shared object 
file: No such file or directory
0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w
but without the path and by loading the modules it runs.
> First do "x lapw0 -p", send t

Re: [Wien] MPI error

[leila mollabashi]

Thank you.

On Mon, May 3, 2021, 3:04 AM Laurence Marks 
wrote:

> You have to solve the "mpirun not found". That is due to your
> path/nfs/module -- we do not know.
>
> ---
> Prof Laurence Marks
> "Research is to see what everyone else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu
>
> On Sun, May 2, 2021, 17:12 leila mollabashi 
> wrote:
>
>> >You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
>> "...:$LD_LIB..."
>>
>> Thank you. I have corrected it but I still have error in x lapw1 “mpirun:
>> command not found”
>>
>> >Why not load the modules in the script to run a job? I have loaded but
>> this error happened “bash: mpirun: command not found”.
>>
>> On Mon, May 3, 2021 at 2:23 AM Laurence Marks 
>> wrote:
>>
>>> You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
>>> "...:$LD_LIB...".
>>>
>>> Why not load the modules in the script to run a job?
>>>
>>> ---
>>> Prof Laurence Marks
>>> "Research is to see what everyone else has seen, and to think what
>>> nobody else has thought", Albert Szent-Györgyi
>>> www.numis.northwestern.edu
>>>
>>> On Sun, May 2, 2021, 16:35 leila mollabashi 
>>> wrote:
>>>
>>>> Dear all WIEN2k users,
>>>>
>>>> Thank you for your reply.
>>>>
>>>> >The error is exactly what it says -- mpirun not found. This has
>>>> something to do with the modules, almost certainly the openmpi one. You
>>>> need to find where mpirun is on your system, and ensure that it is in your
>>>> PATH. This is an issue with your OS, not Wien2k. However...
>>>>
>>>> which mpirun:
>>>>
>>>> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun
>>>>
>>>> I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620,
>>>>  fftw/3.3.8_gcc620 modules. when I added the path in my .bashrc file as
>>>> followes:
>>>>
>>>> export
>>>> LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH
>>>>
>>>> export
>>>> PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH
>>>>
>>>> wien2k does not run:
>>>>
>>>> error while loading shared libraries: libiomp5.so: cannot open shared
>>>> object file: No such file or directory
>>>>
>>>> 0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w
>>>>
>>>> but without the path and by loading the modules it runs.
>>>>
>>>> > First do "x lapw0 -p", send the .machines file and the last few
>>>> lines of your *.output0*. Then we can confirm if that worked right, did not
>>>> or what.
>>>>
>>>> .machines:
>>>>
>>>> lapw0:e0183:4
>>>>
>>>> 1:e0183:4
>>>>
>>>> 1:e0183:4
>>>>
>>>> Almost end of *output:
>>>>
>>>> TOTAL VALUE = -10433.492442 (H)
>>>>
>>>> :DEN  : DENSITY INTEGRAL  =-20866.98488444   (Ry)
>>>>
>>>> Almost end of *output0001
>>>>
>>>> TOTAL VALUE = -10433.492442 (H)
>>>>
>>>> >Assuming that you used gcc
>>>>
>>>> Yes.
>>>>
>>>> >For certain you cannot run lapw2 without first running lapw1.
>>>>
>>>> Yes. You are right. When x lapw1 –p has not executed I have changed the
>>>> .machines file and run in kpoint parallel mode then changed the .machines
>>>> file again and run lapw2 –p.
>>>>
>>>> >How? Do you mean that there are no error messages?
>>>>
>>>> Yes and I also checked compile.msg in SRC_lapw1
>>>>
>>>> Sincerely yours,
>>>>
>>>> Leila
>>>>
>>>>
>>>> On Mon, May 3, 2021 at 12:42 AM Fecher, Gerhard 
>>>> wrote:
>>>>
>>>>> I guess that module does not work with tcsh
>>>>>
>>>>> Ciao
>>>>> Gerhard
>>>>>
>>>>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
>>>>> "I think the problem, t

Re: [Wien] MPI error

[Laurence Marks]

You have to solve the "mpirun not found". That is due to your
path/nfs/module -- we do not know.

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Sun, May 2, 2021, 17:12 leila mollabashi  wrote:

> >You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
> "...:$LD_LIB..."
>
> Thank you. I have corrected it but I still have error in x lapw1 “mpirun:
> command not found”
>
> >Why not load the modules in the script to run a job? I have loaded but
> this error happened “bash: mpirun: command not found”.
>
> On Mon, May 3, 2021 at 2:23 AM Laurence Marks 
> wrote:
>
>> You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
>> "...:$LD_LIB...".
>>
>> Why not load the modules in the script to run a job?
>>
>> ---
>> Prof Laurence Marks
>> "Research is to see what everyone else has seen, and to think what nobody
>> else has thought", Albert Szent-Györgyi
>> www.numis.northwestern.edu
>>
>> On Sun, May 2, 2021, 16:35 leila mollabashi 
>> wrote:
>>
>>> Dear all WIEN2k users,
>>>
>>> Thank you for your reply.
>>>
>>> >The error is exactly what it says -- mpirun not found. This has
>>> something to do with the modules, almost certainly the openmpi one. You
>>> need to find where mpirun is on your system, and ensure that it is in your
>>> PATH. This is an issue with your OS, not Wien2k. However...
>>>
>>> which mpirun:
>>>
>>> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun
>>>
>>> I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620,
>>>  fftw/3.3.8_gcc620 modules. when I added the path in my .bashrc file as
>>> followes:
>>>
>>> export
>>> LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH
>>>
>>> export
>>> PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH
>>>
>>> wien2k does not run:
>>>
>>> error while loading shared libraries: libiomp5.so: cannot open shared
>>> object file: No such file or directory
>>>
>>> 0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w
>>>
>>> but without the path and by loading the modules it runs.
>>>
>>> > First do "x lapw0 -p", send the .machines file and the last few lines
>>> of your *.output0*. Then we can confirm if that worked right, did not or
>>> what.
>>>
>>> .machines:
>>>
>>> lapw0:e0183:4
>>>
>>> 1:e0183:4
>>>
>>> 1:e0183:4
>>>
>>> Almost end of *output:
>>>
>>> TOTAL VALUE = -10433.492442 (H)
>>>
>>> :DEN  : DENSITY INTEGRAL  =-20866.98488444   (Ry)
>>>
>>> Almost end of *output0001
>>>
>>> TOTAL VALUE = -10433.492442 (H)
>>>
>>> >Assuming that you used gcc
>>>
>>> Yes.
>>>
>>> >For certain you cannot run lapw2 without first running lapw1.
>>>
>>> Yes. You are right. When x lapw1 –p has not executed I have changed the
>>> .machines file and run in kpoint parallel mode then changed the .machines
>>> file again and run lapw2 –p.
>>>
>>> >How? Do you mean that there are no error messages?
>>>
>>> Yes and I also checked compile.msg in SRC_lapw1
>>>
>>> Sincerely yours,
>>>
>>> Leila
>>>
>>>
>>> On Mon, May 3, 2021 at 12:42 AM Fecher, Gerhard 
>>> wrote:
>>>
>>>> I guess that module does not work with tcsh
>>>>
>>>> Ciao
>>>> Gerhard
>>>>
>>>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
>>>> "I think the problem, to be quite honest with you,
>>>> is that you have never actually known what the question is."
>>>>
>>>> 
>>>> Dr. Gerhard H. Fecher
>>>> Institut of Physics
>>>> Johannes Gutenberg - University
>>>> 55099 Mainz
>>>> 
>>>> Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von
>>>> Laurence Marks [laurence.ma...@gmail.com]
>>>>

Re: [Wien] MPI error

[leila mollabashi]

>You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
"...:$LD_LIB..."

Thank you. I have corrected it but I still have error in x lapw1 “mpirun:
command not found”

>Why not load the modules in the script to run a job? I have loaded but
this error happened “bash: mpirun: command not found”.

On Mon, May 3, 2021 at 2:23 AM Laurence Marks 
wrote:

> You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
> "...:$LD_LIB...".
>
> Why not load the modules in the script to run a job?
>
> ---
> Prof Laurence Marks
> "Research is to see what everyone else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu
>
> On Sun, May 2, 2021, 16:35 leila mollabashi 
> wrote:
>
>> Dear all WIEN2k users,
>>
>> Thank you for your reply.
>>
>> >The error is exactly what it says -- mpirun not found. This has
>> something to do with the modules, almost certainly the openmpi one. You
>> need to find where mpirun is on your system, and ensure that it is in your
>> PATH. This is an issue with your OS, not Wien2k. However...
>>
>> which mpirun:
>>
>> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun
>>
>> I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620,
>>  fftw/3.3.8_gcc620 modules. when I added the path in my .bashrc file as
>> followes:
>>
>> export
>> LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH
>>
>> export
>> PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH
>>
>> wien2k does not run:
>>
>> error while loading shared libraries: libiomp5.so: cannot open shared
>> object file: No such file or directory
>>
>> 0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w
>>
>> but without the path and by loading the modules it runs.
>>
>> > First do "x lapw0 -p", send the .machines file and the last few lines
>> of your *.output0*. Then we can confirm if that worked right, did not or
>> what.
>>
>> .machines:
>>
>> lapw0:e0183:4
>>
>> 1:e0183:4
>>
>> 1:e0183:4
>>
>> Almost end of *output:
>>
>> TOTAL VALUE = -10433.492442 (H)
>>
>> :DEN  : DENSITY INTEGRAL  =-20866.98488444   (Ry)
>>
>> Almost end of *output0001
>>
>> TOTAL VALUE = -10433.492442 (H)
>>
>> >Assuming that you used gcc
>>
>> Yes.
>>
>> >For certain you cannot run lapw2 without first running lapw1.
>>
>> Yes. You are right. When x lapw1 –p has not executed I have changed the
>> .machines file and run in kpoint parallel mode then changed the .machines
>> file again and run lapw2 –p.
>>
>> >How? Do you mean that there are no error messages?
>>
>> Yes and I also checked compile.msg in SRC_lapw1
>>
>> Sincerely yours,
>>
>> Leila
>>
>>
>> On Mon, May 3, 2021 at 12:42 AM Fecher, Gerhard 
>> wrote:
>>
>>> I guess that module does not work with tcsh
>>>
>>> Ciao
>>> Gerhard
>>>
>>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
>>> "I think the problem, to be quite honest with you,
>>> is that you have never actually known what the question is."
>>>
>>> 
>>> Dr. Gerhard H. Fecher
>>> Institut of Physics
>>> Johannes Gutenberg - University
>>> 55099 Mainz
>>> 
>>> Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von
>>> Laurence Marks [laurence.ma...@gmail.com]
>>> Gesendet: Sonntag, 2. Mai 2021 21:32
>>> An: A Mailing list for WIEN2k users
>>> Betreff: Re: [Wien] MPI error
>>>
>>> Inlined response and questions
>>>
>>> On Sun, May 2, 2021 at 2:19 PM leila mollabashi >> <mailto:le.mollaba...@gmail.com>> wrote:
>>> Dear Prof. Peter Blaha and WIEN2k users,
>>> Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told
>>> me that I can use your script in >
>>> http://www.wien2k.at/reg_user/faq/slurm.job
>>> <https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5s6X8cPOw$>
>>> <
>>> https://urldefense.com/v3/__http://www

Re: [Wien] MPI error

[Laurence Marks]

You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
"...:$LD_LIB...".

Why not load the modules in the script to run a job?

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Sun, May 2, 2021, 16:35 leila mollabashi  wrote:

> Dear all WIEN2k users,
>
> Thank you for your reply.
>
> >The error is exactly what it says -- mpirun not found. This has something
> to do with the modules, almost certainly the openmpi one. You need to find
> where mpirun is on your system, and ensure that it is in your PATH. This is
> an issue with your OS, not Wien2k. However...
>
> which mpirun:
>
> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun
>
> I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620,
>  fftw/3.3.8_gcc620 modules. when I added the path in my .bashrc file as
> followes:
>
> export
> LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH
>
> export
> PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH
>
> wien2k does not run:
>
> error while loading shared libraries: libiomp5.so: cannot open shared
> object file: No such file or directory
>
> 0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w
>
> but without the path and by loading the modules it runs.
>
> > First do "x lapw0 -p", send the .machines file and the last few lines
> of your *.output0*. Then we can confirm if that worked right, did not or
> what.
>
> .machines:
>
> lapw0:e0183:4
>
> 1:e0183:4
>
> 1:e0183:4
>
> Almost end of *output:
>
> TOTAL VALUE = -10433.492442 (H)
>
> :DEN  : DENSITY INTEGRAL  =-20866.98488444   (Ry)
>
> Almost end of *output0001
>
> TOTAL VALUE = -10433.492442 (H)
>
> >Assuming that you used gcc
>
> Yes.
>
> >For certain you cannot run lapw2 without first running lapw1.
>
> Yes. You are right. When x lapw1 –p has not executed I have changed the
> .machines file and run in kpoint parallel mode then changed the .machines
> file again and run lapw2 –p.
>
> >How? Do you mean that there are no error messages?
>
> Yes and I also checked compile.msg in SRC_lapw1
>
> Sincerely yours,
>
> Leila
>
>
> On Mon, May 3, 2021 at 12:42 AM Fecher, Gerhard 
> wrote:
>
>> I guess that module does not work with tcsh
>>
>> Ciao
>> Gerhard
>>
>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
>> "I think the problem, to be quite honest with you,
>> is that you have never actually known what the question is."
>>
>> 
>> Dr. Gerhard H. Fecher
>> Institut of Physics
>> Johannes Gutenberg - University
>> 55099 Mainz
>> 
>> Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von
>> Laurence Marks [laurence.ma...@gmail.com]
>> Gesendet: Sonntag, 2. Mai 2021 21:32
>> An: A Mailing list for WIEN2k users
>> Betreff: Re: [Wien] MPI error
>>
>> Inlined response and questions
>>
>> On Sun, May 2, 2021 at 2:19 PM leila mollabashi > <mailto:le.mollaba...@gmail.com>> wrote:
>> Dear Prof. Peter Blaha and WIEN2k users,
>> Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told
>> me that I can use your script in >
>> http://www.wien2k.at/reg_user/faq/slurm.job
>> <https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5s6X8cPOw$>
>> <
>> https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!G_67ZheBzKx4rn9SJ-7AOPNV2M9DFC6mHQ4b1S_sPZITO1RwQsLYLGNWwENJJwPKlowiXQ$>
>> . I added this lines to it too:
>> module load openmpi/4.1.0_gcc620
>> module load ifort
>> module load mkl
>> but this error happened “bash: mpirun: command not found”.
>> The error is exactly what it says -- mpirun not found. This has something
>> to do with the modules, almost certainly the openmpi one. You need to find
>> where mpirun is on your system, and ensure that it is in your PATH. This is
>> an issue with your OS, not Wien2k. However...
>>
>> In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI but
>> “x lapw1 –p” is stoped with following error:
>> w2k_dispatch_signal(): received: Segmentation fault
>> Is this mpi mode? None

Re: [Wien] MPI error

[leila mollabashi]

Dear all

The admin told me that I can use this line in the script
“/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec
/home/users/SOME_USER/app/my_mpi_app -o option 1 -in
/home/users/SOME_USER/path/to/input1  -o ./output1”

Would you please guide me about this line? Should I use “run_lapw -p”
insead of my_mpi_app? I don’t know what should I do instead of input1
and output1

Sincerely yours,

Leila


On Mon, May 3, 2021 at 2:04 AM leila mollabashi 
wrote:

> Dear all WIEN2k users,
>
> Thank you for your reply.
>
> >The error is exactly what it says -- mpirun not found. This has something
> to do with the modules, almost certainly the openmpi one. You need to find
> where mpirun is on your system, and ensure that it is in your PATH. This is
> an issue with your OS, not Wien2k. However...
>
> which mpirun:
>
> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun
>
> I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620,
>  fftw/3.3.8_gcc620 modules. when I added the path in my .bashrc file as
> followes:
>
> export
> LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH
>
> export
> PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH
>
> wien2k does not run:
>
> error while loading shared libraries: libiomp5.so: cannot open shared
> object file: No such file or directory
>
> 0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w
>
> but without the path and by loading the modules it runs.
>
> > First do "x lapw0 -p", send the .machines file and the last few lines
> of your *.output0*. Then we can confirm if that worked right, did not or
> what.
>
> .machines:
>
> lapw0:e0183:4
>
> 1:e0183:4
>
> 1:e0183:4
>
> Almost end of *output:
>
> TOTAL VALUE = -10433.492442 (H)
>
> :DEN  : DENSITY INTEGRAL  =-20866.98488444   (Ry)
>
> Almost end of *output0001
>
> TOTAL VALUE = -10433.492442 (H)
>
> >Assuming that you used gcc
>
> Yes.
>
> >For certain you cannot run lapw2 without first running lapw1.
>
> Yes. You are right. When x lapw1 –p has not executed I have changed the
> .machines file and run in kpoint parallel mode then changed the .machines
> file again and run lapw2 –p.
>
> >How? Do you mean that there are no error messages?
>
> Yes and I also checked compile.msg in SRC_lapw1
>
> Sincerely yours,
>
> Leila
>
>
> On Mon, May 3, 2021 at 12:42 AM Fecher, Gerhard 
> wrote:
>
>> I guess that module does not work with tcsh
>>
>> Ciao
>> Gerhard
>>
>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
>> "I think the problem, to be quite honest with you,
>> is that you have never actually known what the question is."
>>
>> 
>> Dr. Gerhard H. Fecher
>> Institut of Physics
>> Johannes Gutenberg - University
>> 55099 Mainz
>> 
>> Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von
>> Laurence Marks [laurence.ma...@gmail.com]
>> Gesendet: Sonntag, 2. Mai 2021 21:32
>> An: A Mailing list for WIEN2k users
>> Betreff: Re: [Wien] MPI error
>>
>> Inlined response and questions
>>
>> On Sun, May 2, 2021 at 2:19 PM leila mollabashi > <mailto:le.mollaba...@gmail.com>> wrote:
>> Dear Prof. Peter Blaha and WIEN2k users,
>> Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told
>> me that I can use your script in >
>> http://www.wien2k.at/reg_user/faq/slurm.job<
>> https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!G_67ZheBzKx4rn9SJ-7AOPNV2M9DFC6mHQ4b1S_sPZITO1RwQsLYLGNWwENJJwPKlowiXQ$>
>> . I added this lines to it too:
>> module load openmpi/4.1.0_gcc620
>> module load ifort
>> module load mkl
>> but this error happened “bash: mpirun: command not found”.
>> The error is exactly what it says -- mpirun not found. This has something
>> to do with the modules, almost certainly the openmpi one. You need to find
>> where mpirun is on your system, and ensure that it is in your PATH. This is
>> an issue with your OS, not Wien2k. However...
>>
>> In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI but
>> “x lapw1 –p” is stoped with following error:
>> w2k_dispatch_signal(): received: Segmentation fault
>> Is this mpi mode? None of lapw0/1/2 can work in true parallel without
>> mpirun, so there is something major wrong here. I 

Re: [Wien] MPI error

[leila mollabashi]

Dear all WIEN2k users,

Thank you for your reply.

>The error is exactly what it says -- mpirun not found. This has something
to do with the modules, almost certainly the openmpi one. You need to find
where mpirun is on your system, and ensure that it is in your PATH. This is
an issue with your OS, not Wien2k. However...

which mpirun:

/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun

I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620,
 fftw/3.3.8_gcc620 modules. when I added the path in my .bashrc file as
followes:

export
LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH

export
PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH

wien2k does not run:

error while loading shared libraries: libiomp5.so: cannot open shared
object file: No such file or directory

0.000u 0.000s 0:00.00 0.0%  0+0k 0+0io 0pf+0w

but without the path and by loading the modules it runs.

> First do "x lapw0 -p", send the .machines file and the last few lines of
your *.output0*. Then we can confirm if that worked right, did not or what.

.machines:

lapw0:e0183:4

1:e0183:4

1:e0183:4

Almost end of *output:

TOTAL VALUE = -10433.492442 (H)

:DEN  : DENSITY INTEGRAL  =-20866.98488444   (Ry)

Almost end of *output0001

TOTAL VALUE = -10433.492442 (H)

>Assuming that you used gcc

Yes.

>For certain you cannot run lapw2 without first running lapw1.

Yes. You are right. When x lapw1 –p has not executed I have changed the
.machines file and run in kpoint parallel mode then changed the .machines
file again and run lapw2 –p.

>How? Do you mean that there are no error messages?

Yes and I also checked compile.msg in SRC_lapw1

Sincerely yours,

Leila


On Mon, May 3, 2021 at 12:42 AM Fecher, Gerhard  wrote:

> I guess that module does not work with tcsh
>
> Ciao
> Gerhard
>
> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> "I think the problem, to be quite honest with you,
> is that you have never actually known what the question is."
>
> 
> Dr. Gerhard H. Fecher
> Institut of Physics
> Johannes Gutenberg - University
> 55099 Mainz
> 
> Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von
> Laurence Marks [laurence.ma...@gmail.com]
> Gesendet: Sonntag, 2. Mai 2021 21:32
> An: A Mailing list for WIEN2k users
> Betreff: Re: [Wien] MPI error
>
> Inlined response and questions
>
> On Sun, May 2, 2021 at 2:19 PM leila mollabashi  <mailto:le.mollaba...@gmail.com>> wrote:
> Dear Prof. Peter Blaha and WIEN2k users,
> Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told me
> that I can use your script in >http://www.wien2k.at/reg_user/faq/slurm.job
> <
> https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!G_67ZheBzKx4rn9SJ-7AOPNV2M9DFC6mHQ4b1S_sPZITO1RwQsLYLGNWwENJJwPKlowiXQ$>
> . I added this lines to it too:
> module load openmpi/4.1.0_gcc620
> module load ifort
> module load mkl
> but this error happened “bash: mpirun: command not found”.
> The error is exactly what it says -- mpirun not found. This has something
> to do with the modules, almost certainly the openmpi one. You need to find
> where mpirun is on your system, and ensure that it is in your PATH. This is
> an issue with your OS, not Wien2k. However...
>
> In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI but
> “x lapw1 –p” is stoped with following error:
> w2k_dispatch_signal(): received: Segmentation fault
> Is this mpi mode? None of lapw0/1/2 can work in true parallel without
> mpirun, so there is something major wrong here. I doubt that anything
> really executed properly. For certain you cannot run lapw2 without first
> running lapw1. What is your .machines file? what is the content of the
> error files? (cat *.error).
>
> First do "x lapw0 -p", send the .machines file and the last few lines of
> your *.output0*. Then we can confirm if that worked right, did not or what.
>
> --
> I noticed that the FFTW3 and OpenMPI installed on the cluster are both
> compiled by gfortan. But I have compiled WIEN2k by intel ifort. I am not
> sure whether the problem originates from this inconsistency between gfortan
> and ifort.
> Almost everything in FFTW3 and OpenMPI is in fact c. Assuming that you
> used gcc there should be no problem. In general there should be no problem.
>
> I have checked that lapw1 has compiled correctly.
> How? Do you mean that there are no error messages?
>
>
>

Re: [Wien] MPI error

[Fecher, Gerhard]

I guess that module does not work with tcsh 

Ciao
Gerhard

DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
"I think the problem, to be quite honest with you,
is that you have never actually known what the question is."


Dr. Gerhard H. Fecher
Institut of Physics
Johannes Gutenberg - University
55099 Mainz

Von: Wien [wien-boun...@zeus.theochem.tuwien.ac.at] im Auftrag von Laurence 
Marks [laurence.ma...@gmail.com]
Gesendet: Sonntag, 2. Mai 2021 21:32
An: A Mailing list for WIEN2k users
Betreff: Re: [Wien] MPI error

Inlined response and questions

On Sun, May 2, 2021 at 2:19 PM leila mollabashi 
mailto:le.mollaba...@gmail.com>> wrote:
Dear Prof. Peter Blaha and WIEN2k users,
Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told me that 
I can use your script in 
>http://www.wien2k.at/reg_user/faq/slurm.job<https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!G_67ZheBzKx4rn9SJ-7AOPNV2M9DFC6mHQ4b1S_sPZITO1RwQsLYLGNWwENJJwPKlowiXQ$>
 . I added this lines to it too:
module load openmpi/4.1.0_gcc620
module load ifort
module load mkl
but this error happened “bash: mpirun: command not found”.
The error is exactly what it says -- mpirun not found. This has something to do 
with the modules, almost certainly the openmpi one. You need to find where 
mpirun is on your system, and ensure that it is in your PATH. This is an issue 
with your OS, not Wien2k. However...

In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI but “x 
lapw1 –p” is stoped with following error:
w2k_dispatch_signal(): received: Segmentation fault
Is this mpi mode? None of lapw0/1/2 can work in true parallel without mpirun, 
so there is something major wrong here. I doubt that anything really executed 
properly. For certain you cannot run lapw2 without first running lapw1. What is 
your .machines file? what is the content of the error files? (cat *.error).

First do "x lapw0 -p", send the .machines file and the last few lines of your 
*.output0*. Then we can confirm if that worked right, did not or what.

--
I noticed that the FFTW3 and OpenMPI installed on the cluster are both compiled 
by gfortan. But I have compiled WIEN2k by intel ifort. I am not sure whether 
the problem originates from this inconsistency between gfortan and ifort.
Almost everything in FFTW3 and OpenMPI is in fact c. Assuming that you used gcc 
there should be no problem. In general there should be no problem.

I have checked that lapw1 has compiled correctly.
How? Do you mean that there are no error messages?


Sincerely yours,

Leila



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http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:  
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Re: [Wien] MPI error

[Laurence Marks]

Inlined response and questions

On Sun, May 2, 2021 at 2:19 PM leila mollabashi 
wrote:

> Dear Prof. Peter Blaha and WIEN2k users,
>
> Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told me
> that I can use your script in >http://www.wien2k.at/reg_user/faq/slurm.job
> 
> . I added this lines to it too:
>
> module load openmpi/4.1.0_gcc620
>
> module load ifort
>
> module load mkl
>
> but this error happened “bash: mpirun: command not found”.
>
The error is exactly what it says -- mpirun not found. This has something
to do with the modules, almost certainly the openmpi one. You need to find
where mpirun is on your system, and ensure that it is in your PATH. This is
an issue with your OS, not Wien2k. However...


> In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI but
> “x lapw1 –p” is stoped with following error:
>
> w2k_dispatch_signal(): received: Segmentation fault
>
Is this mpi mode? None of lapw0/1/2 can work in true parallel without
mpirun, so there is something major wrong here. I doubt that anything
really executed properly. For certain you cannot run lapw2 without first
running lapw1. What is your .machines file? what is the content of the
error files? (cat *.error).

First do "x lapw0 -p", send the .machines file and the last few lines of
your *.output0*. Then we can confirm if that worked right, did not or what.

--
>
> I noticed that the FFTW3 and OpenMPI installed on the cluster are both
> compiled by gfortan. But I have compiled WIEN2k by intel ifort. I am not
> sure whether the problem originates from this inconsistency between gfortan
> and ifort.
>
Almost everything in FFTW3 and OpenMPI is in fact c. Assuming that you used
gcc there should be no problem. In general there should be no problem.


> I have checked that lapw1 has compiled correctly.
>
How? Do you mean that there are no error messages?


> Sincerely yours,
>
> Leila
>
>
>
>>
>>
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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] MPI error

[leila mollabashi]

Dear Prof. Peter Blaha and WIEN2k users,

Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told me
that I can use your script in >http://www.wien2k.at/reg_user/faq/slurm.job
. I added this lines to it too:

module load openmpi/4.1.0_gcc620

module load ifort

module load mkl

but this error happened “bash: mpirun: command not found”.

In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI but “x
lapw1 –p” is stoped with following error:

w2k_dispatch_signal(): received: Segmentation fault

--

I noticed that the FFTW3 and OpenMPI installed on the cluster are both
compiled by gfortan. But I have compiled WIEN2k by intel ifort. I am not
sure whether the problem originates from this inconsistency between gfortan
and ifort.

I have checked that lapw1 has compiled correctly.

Sincerely yours,

Leila



On Fri, Apr 23, 2021 at 7:26 PM Peter Blaha 
wrote:

> Recompile with LI, since mpirun is supported (after loading the proper
> mpi).
>
> PS: Ask them if -np and -machinefile is still possible to use. Otherwise
> you cannot mix k-parallel and mpi parallel and for sure, for smaller
> cases it is a severe limitation to have only ONE mpi job with many
> k-points, small matrix size and many mpi cores.
>
> Am 23.04.2021 um 16:04 schrieb leila mollabashi:
> > Dear Prof. Peter Blaha and WIEN2k users,
> >
> > Thank you for your assistances.
> >
> > Here it is the admin reply:
> >
> >   * mpirun/mpiexec command is supported after loadin propper module ( I
> > suggest openmpi/4.1.0 with gcc 6.2.0 or icc )
> >   * you have to describe needed resources (I suggest : --nodes and
> > --ntasks-per-node , please use "whole node" , so ntasks-pper-node=
> > 28 or 32 or 48 , depending of partition)
> >   * Yes, our cluster have "tight integration with mpi" but the
> > other-way-arround : our MPI libraries are compiled with SLURM
> > support, so when you describe resources at the beginning of batch
> > script, you do not have to use "-np" and "-machinefile" options for
> > mpirun/mpiexec
> >
> >   * this error message " btl_openib_component.c:1699:init_one_device" is
> > caused by "old" mpi library, so please recompile your application
> > (WIEN2k) using openmpi/4.1.0_icc19
> >
> > Now should I compile WIEN2k with SL or LI?
> >
> > Sincerely yours,
> >
> > Leila Mollabashi
> >
> >
> > On Wed, Apr 14, 2021 at 10:34 AM Peter Blaha
> > mailto:pbl...@theochem.tuwien.ac.at>>
> wrote:
> >
> > It cannot initialize an mpi job, because it is missing the interface
> > software.
> >
> > You need to ask the computing center / system administrators how one
> > executes a mpi job on this computer.
> >
> > It could be, that "mpirun" is not supported on this machine. You may
> > try
> > a wien2k installation with  system   "LS"  in siteconfig. This will
> > configure the parallel environment/commands using "slurm" commands
> like
> > srun -K -N_nodes_ -n_NP_  ..., replacing mpirun.
> > We used it once on our hpc machine, since it was recommended by the
> > computing center people. However, it turned out that the standard
> > mpirun
> > installation was more stable because the "slurm controller" died too
> > often leading to many random crashes. Anyway, if your system has
> > what is
> > called "tight integration of mpi", it might be necessary.
> >
> > Am 13.04.2021 um 21:47 schrieb leila mollabashi:
> >  > Dear Prof. Peter Blaha and WIEN2k users,
> >  >
> >  > Then by run x lapw1 –p:
> >  >
> >  > starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021
> >  >
> >  > ->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021
> >  >
> >  > running LAPW1 in parallel mode (using .machines)
> >  >
> >  > 2 number_of_parallel_jobs
> >  >
> >  > [1] 14530
> >  >
> >  > [e0467:14538] mca_base_component_repository_open: unable to open
> >  > mca_btl_uct: libucp.so.0: cannot open shared object file: No such
> > file
> >  > or directory (ignored)
> >  >
> >  > WARNING: There was an error initializing an OpenFabrics device.
> >  >
> >  >Local host:   e0467
> >  >
> >  >Local device: mlx4_0
> >  >
> >  > MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> >  >
> >  > with errorcode 0.
> >  >
> >  > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
> processes.
> >  >
> >  > You may or may not see output from other processes, depending on
> >  >
> >  > exactly when Open MPI kills them.
> >  >
> >  >
> >
>  --
> >  >
> >  > [e0467:14567] 1 more process has sent help message
> >  > help-mpi-btl-openib.txt / error in device init
> >  >
> >  > [e0467:14567] 1 more process has sent help message

Re: [Wien] MPI error

[leila mollabashi]

Dear Prof. Peter Blaha and WIEN2k users,

Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told me
that I can use your script in >http://www.wien2k.at/reg_user/faq/slurm.job
. I added this lines to it too:

module load openmpi/4.1.0_gcc620

module load ifort

module load mkl

but this error happened “bash: mpirun: command not found”.

In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI but “x
lapw1 –p” is stoped with following error:

w2k_dispatch_signal(): received: Segmentation fault

--

I noticed that the FFTW3 and OpenMPI installed on the cluster are both
compiled by gfortan. But I have compiled WIEN2k by intel ifort. I am not
sure whether the problem originates from this inconsistency between gfortan
and ifort.

I have checked that lapw1 has compiled correctly.

Sincerely yours,

Leila


On Fri, Apr 23, 2021 at 7:26 PM Peter Blaha 
wrote:

> Recompile with LI, since mpirun is supported (after loading the proper
> mpi).
>
> PS: Ask them if -np and -machinefile is still possible to use. Otherwise
> you cannot mix k-parallel and mpi parallel and for sure, for smaller
> cases it is a severe limitation to have only ONE mpi job with many
> k-points, small matrix size and many mpi cores.
>
> Am 23.04.2021 um 16:04 schrieb leila mollabashi:
> > Dear Prof. Peter Blaha and WIEN2k users,
> >
> > Thank you for your assistances.
> >
> > Here it is the admin reply:
> >
> >   * mpirun/mpiexec command is supported after loadin propper module ( I
> > suggest openmpi/4.1.0 with gcc 6.2.0 or icc )
> >   * you have to describe needed resources (I suggest : --nodes and
> > --ntasks-per-node , please use "whole node" , so ntasks-pper-node=
> > 28 or 32 or 48 , depending of partition)
> >   * Yes, our cluster have "tight integration with mpi" but the
> > other-way-arround : our MPI libraries are compiled with SLURM
> > support, so when you describe resources at the beginning of batch
> > script, you do not have to use "-np" and "-machinefile" options for
> > mpirun/mpiexec
> >
> >   * this error message " btl_openib_component.c:1699:init_one_device" is
> > caused by "old" mpi library, so please recompile your application
> > (WIEN2k) using openmpi/4.1.0_icc19
> >
> > Now should I compile WIEN2k with SL or LI?
> >
> > Sincerely yours,
> >
> > Leila Mollabashi
> >
> >
> > On Wed, Apr 14, 2021 at 10:34 AM Peter Blaha
> > mailto:pbl...@theochem.tuwien.ac.at>>
> wrote:
> >
> > It cannot initialize an mpi job, because it is missing the interface
> > software.
> >
> > You need to ask the computing center / system administrators how one
> > executes a mpi job on this computer.
> >
> > It could be, that "mpirun" is not supported on this machine. You may
> > try
> > a wien2k installation with  system   "LS"  in siteconfig. This will
> > configure the parallel environment/commands using "slurm" commands
> like
> > srun -K -N_nodes_ -n_NP_  ..., replacing mpirun.
> > We used it once on our hpc machine, since it was recommended by the
> > computing center people. However, it turned out that the standard
> > mpirun
> > installation was more stable because the "slurm controller" died too
> > often leading to many random crashes. Anyway, if your system has
> > what is
> > called "tight integration of mpi", it might be necessary.
> >
> > Am 13.04.2021 um 21:47 schrieb leila mollabashi:
> >  > Dear Prof. Peter Blaha and WIEN2k users,
> >  >
> >  > Then by run x lapw1 –p:
> >  >
> >  > starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021
> >  >
> >  > ->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021
> >  >
> >  > running LAPW1 in parallel mode (using .machines)
> >  >
> >  > 2 number_of_parallel_jobs
> >  >
> >  > [1] 14530
> >  >
> >  > [e0467:14538] mca_base_component_repository_open: unable to open
> >  > mca_btl_uct: libucp.so.0: cannot open shared object file: No such
> > file
> >  > or directory (ignored)
> >  >
> >  > WARNING: There was an error initializing an OpenFabrics device.
> >  >
> >  >Local host:   e0467
> >  >
> >  >Local device: mlx4_0
> >  >
> >  > MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> >  >
> >  > with errorcode 0.
> >  >
> >  > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
> processes.
> >  >
> >  > You may or may not see output from other processes, depending on
> >  >
> >  > exactly when Open MPI kills them.
> >  >
> >  >
> >
>  --
> >  >
> >  > [e0467:14567] 1 more process has sent help message
> >  > help-mpi-btl-openib.txt / error in device init
> >  >
> >  > [e0467:14567] 1 more process has sent help message
> 

Re: [Wien] MPI error

[Peter Blaha]

Recompile with LI, since mpirun is supported (after loading the proper mpi).

PS: Ask them if -np and -machinefile is still possible to use. Otherwise 
you cannot mix k-parallel and mpi parallel and for sure, for smaller 
cases it is a severe limitation to have only ONE mpi job with many 
k-points, small matrix size and many mpi cores.


Am 23.04.2021 um 16:04 schrieb leila mollabashi:

Dear Prof. Peter Blaha and WIEN2k users,

Thank you for your assistances.

Here it is the admin reply:

  * mpirun/mpiexec command is supported after loadin propper module ( I
suggest openmpi/4.1.0 with gcc 6.2.0 or icc )
  * you have to describe needed resources (I suggest : --nodes and
--ntasks-per-node , please use "whole node" , so ntasks-pper-node=
28 or 32 or 48 , depending of partition)
  * Yes, our cluster have "tight integration with mpi" but the
other-way-arround : our MPI libraries are compiled with SLURM
support, so when you describe resources at the beginning of batch
script, you do not have to use "-np" and "-machinefile" options for
mpirun/mpiexec

  * this error message " btl_openib_component.c:1699:init_one_device" is
caused by "old" mpi library, so please recompile your application
(WIEN2k) using openmpi/4.1.0_icc19

Now should I compile WIEN2k with SL or LI?

Sincerely yours,

Leila Mollabashi


On Wed, Apr 14, 2021 at 10:34 AM Peter Blaha 
mailto:pbl...@theochem.tuwien.ac.at>> wrote:


It cannot initialize an mpi job, because it is missing the interface
software.

You need to ask the computing center / system administrators how one
executes a mpi job on this computer.

It could be, that "mpirun" is not supported on this machine. You may
try
a wien2k installation with  system   "LS"  in siteconfig. This will
configure the parallel environment/commands using "slurm" commands like
srun -K -N_nodes_ -n_NP_  ..., replacing mpirun.
We used it once on our hpc machine, since it was recommended by the
computing center people. However, it turned out that the standard
mpirun
installation was more stable because the "slurm controller" died too
often leading to many random crashes. Anyway, if your system has
what is
called "tight integration of mpi", it might be necessary.

Am 13.04.2021 um 21:47 schrieb leila mollabashi:
 > Dear Prof. Peter Blaha and WIEN2k users,
 >
 > Then by run x lapw1 –p:
 >
 > starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021
 >
 > ->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021
 >
 > running LAPW1 in parallel mode (using .machines)
 >
 > 2 number_of_parallel_jobs
 >
 > [1] 14530
 >
 > [e0467:14538] mca_base_component_repository_open: unable to open
 > mca_btl_uct: libucp.so.0: cannot open shared object file: No such
file
 > or directory (ignored)
 >
 > WARNING: There was an error initializing an OpenFabrics device.
 >
 >    Local host:   e0467
 >
 >    Local device: mlx4_0
 >
 > MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
 >
 > with errorcode 0.
 >
 > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
 >
 > You may or may not see output from other processes, depending on
 >
 > exactly when Open MPI kills them.
 >
 >
--
 >
 > [e0467:14567] 1 more process has sent help message
 > help-mpi-btl-openib.txt / error in device init
 >
 > [e0467:14567] 1 more process has sent help message
 > help-mpi-btl-openib.txt / error in device init
 >
 > [e0467:14567] Set MCA parameter "orte_base_help_aggregate" to 0
to see
 > all help / error messages
 >
 > [warn] Epoll MOD(1) on fd 27 failed.  Old events were 6; read
change was
 > 0 (none); write change was 2 (del): Bad file descriptor
 >
 >>Somewhere there should be some documentation how one runs an mpi
job on
 > your system.
 >
 > Only I found this:
 >
 > Before ordering a task, it should be encapsulated in an appropriate
 > script understandable for the queue system, e.g .:
 >
 > /home/users/user/submit_script.sl 
>
 >
 > Sample SLURM script:
 >
 > #! / bin / bash -l
 >
 > #SBATCH -N 1
 >
 > #SBATCH --mem 5000
 >
 > #SBATCH --time = 20:00:00
 >
 > /sciezka/do/pliku/binarnego/plik_binarny.in
 >>
 > /sciezka/do/pliku/wyjsciowego.out
 >
 > To order a task to a specific queue, use the #SBATCH -p
parameter, e.g.
 >
 > #! / bin / bash -l
 >
 > #SBATCH -N 1
 >
 > #SBATCH --mem 5000
 >
 > #SBATCH --time = 20:00:00
 >
 > #SBATCH 

Re: [Wien] MPI error

[leila mollabashi]

Dear Prof. Peter Blaha and WIEN2k users,

Thank you for your assistances.

Here it is the admin reply:

   - mpirun/mpiexec command is supported after loadin propper module ( I
   suggest openmpi/4.1.0 with gcc 6.2.0 or icc )
   - you have to describe needed resources (I suggest : --nodes and
   --ntasks-per-node , please use "whole node" , so ntasks-pper-node= 28 or 32
   or 48 , depending of partition)
   - Yes, our cluster have "tight integration with mpi" but the
   other-way-arround : our MPI libraries are compiled with SLURM support, so
   when you describe resources at the beginning of batch script, you do not
   have to use "-np" and "-machinefile" options for mpirun/mpiexec


   - this error message " btl_openib_component.c:1699:init_one_device" is
   caused by "old" mpi library, so please recompile your application (WIEN2k)
   using openmpi/4.1.0_icc19

Now should I compile WIEN2k with SL or LI?

Sincerely yours,

Leila Mollabashi

On Wed, Apr 14, 2021 at 10:34 AM Peter Blaha 
wrote:

> It cannot initialize an mpi job, because it is missing the interface
> software.
>
> You need to ask the computing center / system administrators how one
> executes a mpi job on this computer.
>
> It could be, that "mpirun" is not supported on this machine. You may try
> a wien2k installation with  system   "LS"  in siteconfig. This will
> configure the parallel environment/commands using "slurm" commands like
> srun -K -N_nodes_ -n_NP_  ..., replacing mpirun.
> We used it once on our hpc machine, since it was recommended by the
> computing center people. However, it turned out that the standard mpirun
> installation was more stable because the "slurm controller" died too
> often leading to many random crashes. Anyway, if your system has what is
> called "tight integration of mpi", it might be necessary.
>
> Am 13.04.2021 um 21:47 schrieb leila mollabashi:
> > Dear Prof. Peter Blaha and WIEN2k users,
> >
> > Then by run x lapw1 –p:
> >
> > starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021
> >
> > ->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021
> >
> > running LAPW1 in parallel mode (using .machines)
> >
> > 2 number_of_parallel_jobs
> >
> > [1] 14530
> >
> > [e0467:14538] mca_base_component_repository_open: unable to open
> > mca_btl_uct: libucp.so.0: cannot open shared object file: No such file
> > or directory (ignored)
> >
> > WARNING: There was an error initializing an OpenFabrics device.
> >
> >Local host:   e0467
> >
> >Local device: mlx4_0
> >
> > MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> >
> > with errorcode 0.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> >
> > You may or may not see output from other processes, depending on
> >
> > exactly when Open MPI kills them.
> >
> >
> --
> >
> > [e0467:14567] 1 more process has sent help message
> > help-mpi-btl-openib.txt / error in device init
> >
> > [e0467:14567] 1 more process has sent help message
> > help-mpi-btl-openib.txt / error in device init
> >
> > [e0467:14567] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> > all help / error messages
> >
> > [warn] Epoll MOD(1) on fd 27 failed.  Old events were 6; read change was
> > 0 (none); write change was 2 (del): Bad file descriptor
> >
> >>Somewhere there should be some documentation how one runs an mpi job on
> > your system.
> >
> > Only I found this:
> >
> > Before ordering a task, it should be encapsulated in an appropriate
> > script understandable for the queue system, e.g .:
> >
> > /home/users/user/submit_script.sl 
> >
> > Sample SLURM script:
> >
> > #! / bin / bash -l
> >
> > #SBATCH -N 1
> >
> > #SBATCH --mem 5000
> >
> > #SBATCH --time = 20:00:00
> >
> > /sciezka/do/pliku/binarnego/plik_binarny.in >
> > /sciezka/do/pliku/wyjsciowego.out
> >
> > To order a task to a specific queue, use the #SBATCH -p parameter, e.g.
> >
> > #! / bin / bash -l
> >
> > #SBATCH -N 1
> >
> > #SBATCH --mem 5000
> >
> > #SBATCH --time = 20:00:00
> >
> > #SBATCH -p standard
> >
> > /sciezka/do/pliku/binarnego/plik_binarny.in >
> > /siezka/do/pliku/wyjsciowego.out
> >
> > The task must then be ordered using the *sbatch* command
> >
> > sbatch /home/users/user/submit_script.sl 
> >
> > *Ordering interactive tasks***
> >
> >
> > Interactive tasks can be divided into two groups:
> >
> > ·interactive task (working in text mode)
> >
> > ·interactive task
> >
> > *Interactive task (working in text mode)***
> >
> >
> > Ordering interactive tasks is very simple and in the simplest case it
> > comes down to issuing the command below.
> >
> > srun --pty / bin / bash
> >
> > Sincerely yours,
> >
> > Leila Mollabashi
> >
> >
> > On Wed, Apr 14, 2021 at 12:03 AM leila mollabashi
> > mailto:le.mollaba...@gmail.com>> wrote:
> >
> > Dear Prof. Peter Blaha and WIEN2k 

Re: [Wien] MPI error

[Peter Blaha]

It cannot initialize an mpi job, because it is missing the interface 
software.


You need to ask the computing center / system administrators how one 
executes a mpi job on this computer.


It could be, that "mpirun" is not supported on this machine. You may try 
a wien2k installation with  system   "LS"  in siteconfig. This will 
configure the parallel environment/commands using "slurm" commands like 
srun -K -N_nodes_ -n_NP_  ..., replacing mpirun.
We used it once on our hpc machine, since it was recommended by the 
computing center people. However, it turned out that the standard mpirun 
installation was more stable because the "slurm controller" died too 
often leading to many random crashes. Anyway, if your system has what is 
called "tight integration of mpi", it might be necessary.


Am 13.04.2021 um 21:47 schrieb leila mollabashi:

Dear Prof. Peter Blaha and WIEN2k users,

Then by run x lapw1 –p:

starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021

->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021

running LAPW1 in parallel mode (using .machines)

2 number_of_parallel_jobs

[1] 14530

[e0467:14538] mca_base_component_repository_open: unable to open 
mca_btl_uct: libucp.so.0: cannot open shared object file: No such file 
or directory (ignored)


WARNING: There was an error initializing an OpenFabrics device.

   Local host:   e0467

   Local device: mlx4_0

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD

with errorcode 0.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--

[e0467:14567] 1 more process has sent help message 
help-mpi-btl-openib.txt / error in device init


[e0467:14567] 1 more process has sent help message 
help-mpi-btl-openib.txt / error in device init


[e0467:14567] Set MCA parameter "orte_base_help_aggregate" to 0 to see 
all help / error messages


[warn] Epoll MOD(1) on fd 27 failed.  Old events were 6; read change was 
0 (none); write change was 2 (del): Bad file descriptor



Somewhere there should be some documentation how one runs an mpi job on

your system.

Only I found this:

Before ordering a task, it should be encapsulated in an appropriate 
script understandable for the queue system, e.g .:


/home/users/user/submit_script.sl 

Sample SLURM script:

#! / bin / bash -l

#SBATCH -N 1

#SBATCH --mem 5000

#SBATCH --time = 20:00:00

/sciezka/do/pliku/binarnego/plik_binarny.in > 
/sciezka/do/pliku/wyjsciowego.out


To order a task to a specific queue, use the #SBATCH -p parameter, e.g.

#! / bin / bash -l

#SBATCH -N 1

#SBATCH --mem 5000

#SBATCH --time = 20:00:00

#SBATCH -p standard

/sciezka/do/pliku/binarnego/plik_binarny.in > 
/siezka/do/pliku/wyjsciowego.out


The task must then be ordered using the *sbatch* command

sbatch /home/users/user/submit_script.sl 

*Ordering interactive tasks***


Interactive tasks can be divided into two groups:

·interactive task (working in text mode)

·interactive task

*Interactive task (working in text mode)***


Ordering interactive tasks is very simple and in the simplest case it 
comes down to issuing the command below.


srun --pty / bin / bash

Sincerely yours,

Leila Mollabashi


On Wed, Apr 14, 2021 at 12:03 AM leila mollabashi 
mailto:le.mollaba...@gmail.com>> wrote:


Dear Prof. Peter Blaha and WIEN2k users,

Thank you for your assistances.

>  At least now the error: "lapw0 not found" is gone. Do you
understand why ??

Yes, I think that because now the path is clearly known.

>How many slots do you get by this srun command ?

Usually I went to node with 28 CPUs.

>Is this the node with the name  e0591 ???

Yes, it is.

>Of course the .machines file must be consistent (dynamically adapted)

with the actual nodename.

Yes, to do this I use my script.

>When I  use “srun --pty -n 8 /bin/bash” that goes to the node with 8 free
cores, and run x lapw0 –p then this happens:

starting parallel lapw0 at Tue Apr 13 20:50:49 CEST 2021

 .machine0 : 4 processors

[1] 12852

[e0467:12859] mca_base_component_repository_open: unable to open
mca_btl_uct: libucp.so.0: cannot open shared object file: No such
file or directory (ignored)

[e0467][[56319,1],1][btl_openib_component.c:1699:init_one_device]
error obtaining device attributes for mlx4_0 errno says Protocol not
supported

[e0467:12859] mca_base_component_repository_open: unable to open
mca_pml_ucx: libucp.so.0: cannot open shared object file: No such
file or directory (ignored)

LAPW0 END

[1]    Done  mpirun -np 4 -machinefile
.machine0 /home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >> .time00

Sincerely 

Re: [Wien] MPI error

[leila mollabashi]

Dear Prof. Peter Blaha and WIEN2k users,

Then by run x lapw1 –p:

starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021

->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021

running LAPW1 in parallel mode (using .machines)

2 number_of_parallel_jobs

[1] 14530

[e0467:14538] mca_base_component_repository_open: unable to open
mca_btl_uct: libucp.so.0: cannot open shared object file: No such file or
directory (ignored)

WARNING: There was an error initializing an OpenFabrics device.

  Local host:   e0467

  Local device: mlx4_0

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD

with errorcode 0.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--

[e0467:14567] 1 more process has sent help message help-mpi-btl-openib.txt
/ error in device init

[e0467:14567] 1 more process has sent help message help-mpi-btl-openib.txt
/ error in device init

[e0467:14567] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages

[warn] Epoll MOD(1) on fd 27 failed.  Old events were 6; read change was 0
(none); write change was 2 (del): Bad file descriptor

>Somewhere there should be some documentation how one runs an mpi job on
your system.

Only I found this:

Before ordering a task, it should be encapsulated in an appropriate script
understandable for the queue system, e.g .:

/home/users/user/submit_script.sl

Sample SLURM script:

#! / bin / bash -l

#SBATCH -N 1

#SBATCH --mem 5000

#SBATCH --time = 20:00:00



/sciezka/do/pliku/binarnego/plik_binarny.in>
/sciezka/do/pliku/wyjsciowego.out

To order a task to a specific queue, use the #SBATCH -p parameter, e.g.

#! / bin / bash -l

#SBATCH -N 1

#SBATCH --mem 5000

#SBATCH --time = 20:00:00

#SBATCH -p standard



/sciezka/do/pliku/binarnego/plik_binarny.in>
/siezka/do/pliku/wyjsciowego.out

The task must then be ordered using the *sbatch* command

sbatch /home/users/user/submit_script.sl

*Ordering interactive tasks*


Interactive tasks can be divided into two groups:

· interactive task (working in text mode)

· interactive task

*Interactive task (working in text mode)*


Ordering interactive tasks is very simple and in the simplest case it comes
down to issuing the command below.

srun --pty / bin / bash



Sincerely yours,

Leila Mollabashi

On Wed, Apr 14, 2021 at 12:03 AM leila mollabashi 
wrote:

> Dear Prof. Peter Blaha and WIEN2k users,
>
> Thank you for your assistances.
>
> > At least now the error: "lapw0 not found" is gone. Do you understand
> why ??
>
> Yes, I think that because now the path is clearly known.
>
> >How many slots do you get by this srun command ?
>
> Usually I went to node with 28 CPUs.
>
> >Is this the node with the name  e0591  ???
>
> Yes, it is.
>
> >Of course the .machines file must be consistent (dynamically adapted)
>
> with the actual nodename.
>
> Yes, to do this I use my script.
>
> >When I use “srun --pty -n 8 /bin/bash” that goes to the node with 8 free
> cores, and run x lapw0 –p then this happens:
>
> starting parallel lapw0 at Tue Apr 13 20:50:49 CEST 2021
>
>  .machine0 : 4 processors
>
> [1] 12852
>
> [e0467:12859] mca_base_component_repository_open: unable to open
> mca_btl_uct: libucp.so.0: cannot open shared object file: No such file or
> directory (ignored)
>
> [e0467][[56319,1],1][btl_openib_component.c:1699:init_one_device] error
> obtaining device attributes for mlx4_0 errno says Protocol not supported
>
> [e0467:12859] mca_base_component_repository_open: unable to open
> mca_pml_ucx: libucp.so.0: cannot open shared object file: No such file or
> directory (ignored)
>
> LAPW0 END
>
> [1]Done  mpirun -np 4 -machinefile .machine0
> /home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >> .time00
>
> Sincerely yours,
>
> Leila Mollabashi
>
>
>
___
Wien mailing list
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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] MPI error

[Peter Blaha]

Am 12.04.2021 um 20:00 schrieb leila mollabashi:

Dear Prof. Peter Blaha and WIEN2k users,

Thank you. Now my .machines file is:

lapw0:e0591:4

1:e0591:4

1:e0591:4

granularity:1

extrafine:1

I have installed WIEN2k in my user in the cluster. When I use this 
script “srun --pty /bin/bash” then it goes to one node of the cluster, 
the “ls -als $WIENROOT/lapw0”, “x lapw0” and “lapw0 lapw0.def” commands 
are executed but, “x lapw0 –p” is not executed.The following error appears:


At least now the error: "lapw0 not found" is gone. Do you understand why ??

So you opened an interactive session on one node.
How many slots do you get by this srun command ?
Is this the node with the name  e0591  ???
Of course the .machines file must be consistent (dynamically adapted) 
with the actual nodename.


As you could see at the bottom of the message, the command

x lapw0 -p

creates   lapw0.def and .machine0, but then executes

mpirun -np 4 -machinefile .machine0


Somewhere there should be some documentation how one runs an mpi job on 
your system.


It is almost impossible to solve this from outside. All we can do is 
giving some tips.




There are not enough slots available in the system to satisfy the 4

slots that were requested by the application:

   /home/users/mollabashi/v19.2/lapw0_mpi

Either request fewer slots for your application, or make more slots

available for use.

A "slot" is the Open MPI term for an allocatable unit where we can

launch a process.  The number of slots available are defined by the

environment in which Open MPI processes are run:

   1. Hostfile, via "slots=N" clauses (N defaults to number of

  processor cores if not provided)

   2. The --host command line parameter, via a ":N" suffix on the

  hostname (N defaults to 1 if not provided)

   3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)

   4. If none of a hostfile, the --host command line parameter, or an

  RM is present, Open MPI defaults to the number of processor cores

In all the above cases, if you want Open MPI to default to the number

of hardware threads instead of the number of processor cores, use the

--use-hwthread-cpus option.

Alternatively, you can use the --oversubscribe option to ignore the

number of available slots when deciding the number of processes to

launch.

--

[1]    Exit 1    mpirun -np 4 -machinefile .machine0 
/home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >> .time00


0.067u 0.091s 0:02.97 5.0%  0+0k 52272+144io 54pf+0w

mollabashi@eagle:~/test1/cein$ cat .machines

Sincerely yours,

Leila Mollabashi


On Sun, Apr 11, 2021 at 9:40 PM Peter Blaha 
mailto:pbl...@theochem.tuwien.ac.at>> wrote:


Your script is still wrong.
The .machines file should show:

lapw0:e0150:4

not
lapw0:e0150
:4

Therefore it tries to execute lapw0 instead of lapw0_mpi.
---
Anyway, the first thing is to make the sequential wien2k running. You
claimed the WIENROOT is known in the batch job.
Please do:
ls -als $WIENROOT/lapw0

Does it have execute permission ?

If yes, execute lapw0 explicitly:

x lapw0

and a second time:

lapw0 lapw0.def


Am 11.04.2021 um 13:17 schrieb leila mollabashi:
 > Dear Prof. Peter Blaha,
 >
 > Thank you for your guides. You are right. I edited the script and
added
 > “source ~/.bashrc, echo 'lapw0:'`hostname`' :'$nproc >>
.machines” to it.
 >
 > The crated .machines file is as follows:
 >
 > lapw0:e0150
 >
 > :4
 >
 > 1:e0150:4
 >
 > 1:e0150:4
 >
 > granularity:1
 >
 > extrafine:1
 >
 > The slurm.out file is:
 >
 > e0150
 >
 > # .machines
 >
 > bash: lapw0: command not found
 >
 > real 0m0.001s
 >
 > user 0m0.001s
 >
 > sys 0m0.000s
 >
 > grep: *scf1*: No such file or directory
 >
 > grep: lapw2*.error: No such file or directory
 >
 >>  stop error
 >
 > When I used the following commands:
 >
 > echo $WIENROOT
 > which lapw0
 > which lapw0_mpi
 >
 > The following paths were printed:
 >
 > /home/users/mollabashi/v19.2
 >
 > /home/users/mollabashi/v19.2/lapw0
 >
 > /home/users/mollabashi/v19.2/lapw0_mpi
 >
 > But the error is still exists:
 >
 > bash: lapw0: command not found
 >
 > When I used your script in (faq page), one time the .machines
file was
 > generated.
 >
 > But it stopped due to an error.
 >
 > test.scf1_1: No such file or directory.
 >
 > grep: *scf1*: No such file or directory
 >
 > FERMI - Error
 >
 > When I loaded openmpi and ifort as well as icc in the script this
error
 > appeared:
 >
 >>SLURM_NTASKS_PER_NODE:  Undefined variable.
 >
 > Every time after that the
 >

Re: [Wien] MPI error

[leila mollabashi]

Dear Prof. Peter Blaha and WIEN2k users,

Thank you. Now my .machines file is:

lapw0:e0591:4

1:e0591:4

1:e0591:4

granularity:1

extrafine:1

I have installed WIEN2k in my user in the cluster. When I use this script “srun
--pty /bin/bash” then it goes to one node of the cluster, the “ls -als
$WIENROOT/lapw0”, “x lapw0” and “lapw0 lapw0.def” commands are executed
but, “x lapw0 –p” is not executed. The following error appears:

There are not enough slots available in the system to satisfy the 4

slots that were requested by the application:

  /home/users/mollabashi/v19.2/lapw0_mpi

Either request fewer slots for your application, or make more slots

available for use.

A "slot" is the Open MPI term for an allocatable unit where we can

launch a process.  The number of slots available are defined by the

environment in which Open MPI processes are run:

  1. Hostfile, via "slots=N" clauses (N defaults to number of

 processor cores if not provided)

  2. The --host command line parameter, via a ":N" suffix on the

 hostname (N defaults to 1 if not provided)

  3. Resource manager (e.g., SLURM, PBS/Torque, LSF, etc.)

  4. If none of a hostfile, the --host command line parameter, or an

 RM is present, Open MPI defaults to the number of processor cores

In all the above cases, if you want Open MPI to default to the number

of hardware threads instead of the number of processor cores, use the

--use-hwthread-cpus option.

Alternatively, you can use the --oversubscribe option to ignore the

number of available slots when deciding the number of processes to

launch.

--

[1]Exit 1mpirun -np 4 -machinefile .machine0
/home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >> .time00

0.067u 0.091s 0:02.97 5.0%  0+0k 52272+144io 54pf+0w

mollabashi@eagle:~/test1/cein$ cat .machines

Sincerely yours,

Leila Mollabashi

On Sun, Apr 11, 2021 at 9:40 PM Peter Blaha 
wrote:

> Your script is still wrong.
> The .machines file should show:
>
> lapw0:e0150:4
>
> not
> lapw0:e0150
> :4
>
> Therefore it tries to execute lapw0 instead of lapw0_mpi.
> ---
> Anyway, the first thing is to make the sequential wien2k running. You
> claimed the WIENROOT is known in the batch job.
> Please do:
> ls -als $WIENROOT/lapw0
>
> Does it have execute permission ?
>
> If yes, execute lapw0 explicitly:
>
> x lapw0
>
> and a second time:
>
> lapw0 lapw0.def
>
>
> Am 11.04.2021 um 13:17 schrieb leila mollabashi:
> > Dear Prof. Peter Blaha,
> >
> > Thank you for your guides. You are right. I edited the script and added
> > “source ~/.bashrc, echo 'lapw0:'`hostname`' :'$nproc >> .machines” to it.
> >
> > The crated .machines file is as follows:
> >
> > lapw0:e0150
> >
> > :4
> >
> > 1:e0150:4
> >
> > 1:e0150:4
> >
> > granularity:1
> >
> > extrafine:1
> >
> > The slurm.out file is:
> >
> > e0150
> >
> > # .machines
> >
> > bash: lapw0: command not found
> >
> > real 0m0.001s
> >
> > user 0m0.001s
> >
> > sys 0m0.000s
> >
> > grep: *scf1*: No such file or directory
> >
> > grep: lapw2*.error: No such file or directory
> >
> >>  stop error
> >
> > When I used the following commands:
> >
> > echo $WIENROOT
> > which lapw0
> > which lapw0_mpi
> >
> > The following paths were printed:
> >
> > /home/users/mollabashi/v19.2
> >
> > /home/users/mollabashi/v19.2/lapw0
> >
> > /home/users/mollabashi/v19.2/lapw0_mpi
> >
> > But the error is still exists:
> >
> > bash: lapw0: command not found
> >
> > When I used your script in (faq page), one time the .machines file was
> > generated.
> >
> > But it stopped due to an error.
> >
> > test.scf1_1: No such file or directory.
> >
> > grep: *scf1*: No such file or directory
> >
> > FERMI - Error
> >
> > When I loaded openmpi and ifort as well as icc in the script this error
> > appeared:
> >
> >>SLURM_NTASKS_PER_NODE:  Undefined variable.
> >
> > Every time after that the
> >
> >>SLURM_NTASKS_PER_NODE:  Undefined variable
> >
> >   error happened when I used your scripts without changing it. I have
> > tried several times even in a new directory with no positive effect.
> >
> >>SLURM_NTASKS_PER_NODE:  Undefined variable.
> >
> > Sincerely yours,
> >
> > Leila Mollabashi
> >
> >
> > ___
> > 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
> >
>
> --
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at
> -
> ___
> 

Re: [Wien] MPI error

[Peter Blaha]

Your script is still wrong.
The .machines file should show:

lapw0:e0150:4

not
lapw0:e0150
:4

Therefore it tries to execute lapw0 instead of lapw0_mpi.
---
Anyway, the first thing is to make the sequential wien2k running. You 
claimed the WIENROOT is known in the batch job.

Please do:
ls -als $WIENROOT/lapw0

Does it have execute permission ?

If yes, execute lapw0 explicitly:

x lapw0

and a second time:

lapw0 lapw0.def


Am 11.04.2021 um 13:17 schrieb leila mollabashi:

Dear Prof. Peter Blaha,

Thank you for your guides. You are right. I edited the script and added 
“source ~/.bashrc, echo 'lapw0:'`hostname`' :'$nproc >> .machines” to it.


The crated .machines file is as follows:

lapw0:e0150

:4

1:e0150:4

1:e0150:4

granularity:1

extrafine:1

The slurm.out file is:

e0150

# .machines

bash: lapw0: command not found

real 0m0.001s

user 0m0.001s

sys 0m0.000s

grep: *scf1*: No such file or directory

grep: lapw2*.error: No such file or directory


 stop error


When I used the following commands:

echo $WIENROOT
which lapw0
which lapw0_mpi

The following paths were printed:

/home/users/mollabashi/v19.2

/home/users/mollabashi/v19.2/lapw0

/home/users/mollabashi/v19.2/lapw0_mpi

But the error is still exists:

bash: lapw0: command not found

When I used your script in (faq page), one time the .machines file was 
generated.


But it stopped due to an error.

test.scf1_1: No such file or directory.

grep: *scf1*: No such file or directory

FERMI - Error

When I loaded openmpi and ifort as well as icc in the script this error 
appeared:



SLURM_NTASKS_PER_NODE:  Undefined variable.


Every time after that the


SLURM_NTASKS_PER_NODE:  Undefined variable


  error happened when I used your scripts without changing it. I have 
tried several times even in a new directory with no positive effect.



SLURM_NTASKS_PER_NODE:  Undefined variable.


Sincerely yours,

Leila Mollabashi


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Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
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