Yambo Community Forum

Posted: **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.

Posted: **Wed Apr 19, 2023 8:24 am**

Dear Daniele and Davide,

When I do install Yambo5.1.1 on Nersc Cori.

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$ 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

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$ ./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

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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".

Posted: **Wed Apr 19, 2023 8:30 am**

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

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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.

Posted: **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

Posted: **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

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