Yambo5.1.1 Tddft ALDA run error

Deals with issues related to computation of optical spectra in reciprocal space: RPA, TDDFT, local field effects.

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Davide Sangalli
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Re: Yambo5.1.1 Tddft ALDA run error

Post by Davide Sangalli » Wed Apr 19, 2023 7:54 am

However, I tried to install Yambo 5.1.1 on Nersc cluster. It shows the same errors when run it.
Just to understand, which error: at configure time or at running time?

To provide we need to have clear info on configuration, installation and run.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

hongtang2023
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Re: Yambo5.1.1 Tddft ALDA run error

Post by hongtang2023 » Wed Apr 19, 2023 8:24 am

Dear Daniele and Davide,

When I do install Yambo5.1.1 on Nersc Cori.

Code: Select all

$ module list
Currently Loaded Modulefiles:
  1) modules/3.2.11.4
  2) darshan/3.4.0
  3) craype-network-aries
  4) intel/19.1.2.254
  5) craype/2.7.10
  6) cray-libsci/20.09.1
  7) udreg/2.3.2-7.0.3.1_3.41__g5f0d670.ari
  8) ugni/6.0.14.0-7.0.3.1_6.23__g8101a58.ari
  9) pmi/5.0.17
 10) dmapp/7.1.1-7.0.3.1_3.42__g93a7e9f.ari
 11) gni-headers/5.0.12.0-7.0.3.1_3.25__gd0d73fe.ari
 12) xpmem/2.2.27-7.0.3.1_3.26__gada73ac.ari
 13) job/2.2.4-7.0.3.1_3.33__g36b56f4.ari
 14) dvs/2.12_2.2.224-7.0.3.1_3.32__gc77db2af
 15) alps/6.6.67-7.0.3.1_3.41__gb91cd181.ari
 16) rca/2.2.20-7.0.3.1_3.44__g8e3fb5b.ari
 17) atp/3.14.9
 18) perftools-base/21.12.0
 19) PrgEnv-intel/6.0.10
 20) craype-haswell
 21) cray-mpich/7.7.19
 22) craype-hugepages2M
then I do

Code: Select all

$ ./configure --enable-mpi --enable-open-mp --enable-open-mp --enable-memory-profile
then
make all
please see attached config.log file.



the I run it as

Code: Select all

srun -n 32 -c 32 --cpu_bind=cores    yambo  -F  run_in_ALDA   -J alda_q100 


thenI got error

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 <01h-00m> [DIP] Writing dipoles header
[ERROR] STOP signal received while in[04] Dipoles
[ERROR] Writing File ./alda_q100//ndb.dipoles; Variable  NOT DEFINED; Permission denied

I checked on Nersc Cori cluster. I cannot find mpicc, mpifort, mpiifort or mpif90.
I only find icc, ifort, gcc (7.5.0), gfortran. I also find ftn, which is for cray.
Nersc clusters use "srun" for submit jobs, instead of "mpirun".
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Dr. Hong Tang
Tulane University
New Orleans, LA
70118, USA

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Davide Sangalli
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Re: Yambo5.1.1 Tddft ALDA run error

Post by Davide Sangalli » Wed Apr 19, 2023 8:30 am

The issue is that you are compiling yamob in serial.
See this line in the configure:

Code: Select all

configure:8971: WARNING: could not compile a FORTRAN mpi test program. YAMBO serial only.
Accordingly you cannot run yambo in parallel.

You need to figure our which is the parallel compiler on nersc and the associated module to be loaded.
The configure tried these ones, and none of them worked

Code: Select all

configure:8743: checking for mpipgifort
configure:8773: result: no
configure:8743: checking for mpiifort
configure:8773: result: no
configure:8743: checking for mpifort
configure:8773: result: no
configure:8743: checking for mpif90
configure:8773: result: no
configure:8743: checking for mpxlf90
configure:8773: result: no
configure:8743: checking for mpxlf
configure:8773: result: no
configure:8743: checking for mpf90
configure:8773: result: no
configure:8743: checking for mpxlf95
configure:8773: result: no
configure:8743: checking for mpxlf_r
configure:8773: result: no
You can probably ask for support to the nersc cluster directly.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

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Daniele Varsano
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Re: Yambo5.1.1 Tddft ALDA run error

Post by Daniele Varsano » Mon Apr 24, 2023 8:51 am

Dear Hong,
can you please post the config.log file when trying to install Yambo at NERSC?

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

hongtang2023
Posts: 45
Joined: Thu Mar 16, 2023 7:02 am

Re: Yambo5.1.1 Tddft ALDA run error

Post by hongtang2023 » Mon Apr 24, 2023 6:31 pm

Dear Daniele,

Thank you for helping!
The installation of Yambo5.1.1 on Nersc cluster is OK now. The Cray mpich in Nersc cluster is a little bit different from mpi/openmp. It is ok now.

Best,
Hong
Dr. Hong Tang
Tulane University
New Orleans, LA
70118, USA

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