[QE-users] Error in neb.x calculation on Cedar cluster

[Paolo Giannozzi]

On Mon, Apr 5, 2021 at 4:33 AM Dr. K. C. Bhamu <kcbhamu85 at gmail.com> wrote:

Replace -i with -inp
>

this cannot have any effect: -i, -in, -inp are all accepted.

It is impossible to say anything without more and better information.

Paolo

On Mon, Apr 5, 2021, 07:29 Rutika Savaliya <rutika.savaliya at mail.mcgill.ca>
> wrote:
>
>> Hello
>> My name is Rutika, user srutika. I run quantum espresso calculation on
>> the Cedar cluster. The Job script is located /scratch/srutika. While neb.x
>> calculation is running into the same issue after starting. It started after
>> recent changes on computecanada. My run.sh file and error appearing is
>> as below:
>>
>> #!/bin/sh
>> #SBATCH --nodes=6
>> #SBATCH --ntasks-per-node=48
>> #SBATCH --time=08-00:00
>> #MPI tasks
>> #SBATCH --mem=0
>> #SBATCH --account=def-jkopysci
>>
>> module load quantumespresso/6.5
>>
>> srun neb.x -i RR8.in > RR8.out
>>
>>
>> My error is as below:
>>
>> [cdr2189:54345] *** An error occurred in MPI_Type_free
>> [cdr2189:54345] *** reported by process [500170752,196]
>> [cdr2189:54345] *** on communicator MPI_COMM_WORLD
>> [cdr2189:54345] *** MPI_ERR_TYPE: invalid datatype
>> [cdr2189:54345] *** MPI_ERRORS_ARE_FATAL (processes in this communicator
>> will now abort,
>> [cdr2189:54345] ***    and potentially your MPI job)
>> In: PMI_Abort(3, N/A)
>> slurmstepd: error: *** STEP 65543632.0 ON cdr2092 CANCELLED AT
>> 2021-04-04T13:58:54 ***
>> srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
>> srun: error: cdr2106: tasks 96-143: Killed
>> srun: launch/slurm: _step_signal: Terminating StepId=65543632.0
>> srun: error: cdr2096: tasks 48-95: Killed
>> srun: error: cdr2159: tasks 144-191: Killed
>> srun: error: cdr2189: tasks 192-195,197-239: Killed
>> srun: error: cdr2092: tasks 0-47: Killed
>> srun: error: cdr2190: tasks 240-287: Killed
>> srun: error: cdr2189: task 196: Exited with exit code 3
>>
>>
>> I have also attached the slurm file for reference.
>>
>> Hope to find the solution for this issue.
>>
>> Thank You.
>> Rutika
>> _______________________________________________
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>
> _______________________________________________
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-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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