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
<pbl...@theochem.tuwien.ac.at <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
>
>>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
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.at
<mailto:bl...@theochem.tuwien.ac.at> WIEN2k: http://www.wien2k.at
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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.at WIEN2k: http://www.wien2k.at
WWW: http://www.imc.tuwien.ac.at
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