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Re: Yambo5.1.1 Tddft ALDA run error
Posted: Wed Apr 19, 2023 7:54 am
by Davide Sangalli
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.
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Wed Apr 19, 2023 8:24 am
by hongtang2023
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
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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".
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Wed Apr 19, 2023 8:30 am
by Davide Sangalli
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.
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Mon Apr 24, 2023 8:51 am
by Daniele Varsano
Dear Hong,
can you please post the config.log file when trying to install Yambo at NERSC?
Best,
Daniele
Re: Yambo5.1.1 Tddft ALDA run error
Posted: Mon Apr 24, 2023 6:31 pm
by hongtang2023
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