I'm an adimistrator for our University HPC-System and was told to set up Yambo 4.0.1 for our UniversalCluster.
AND: I'm not a scientist so I'm not familiar with Yambo at all
Unfortunately I get this error-message when I try to run the MPI-example you supplied at your homepage:
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<01s> [01] CPU structure, Files & I/O Directories
<01s> [02] CORE Variables Setup
<01s> [02.01] Unit cells
<01s> [02.02] Symmetries
<01s> [02.03] RL shells
<01s> [02.04] K-grid lattice
<01s> [02.05] Energies [ev] & Occupations
<01s> [03] Transferred momenta grid
<01s> [04] External corrections
<02s> [05] Dynamic Dielectric Matrix (PPA)
<03s> [M 0.203 Gb] Alloc WF ( 0.188)
<03s> [WF] Performing Wave-Functions I/O
<04s> [M 0.203 Gb] Free wf_disk ( 0.011)
<04s> [X-CG] R(p) Tot o/o(of R) : 1925 3750 100
<04s> Xo@q[1] | | [000%] --(E) --(X)
<09s> Xo@q[1] |############################# | [073%] 05s(E) 06s(X)
<11s> Xo@q[1] |########################################| [100%] 06s(E) 06s(X)
<11s> X@q[1] | | [000%] --(E) --(X)
<11s> X@q[1] |########################################| [100%] --(E) --(X)
<12s> [M 0.010 Gb] Free WF ( 0.188)
<12s> [06] Bare local and non-local Exchange-Correlation
<13s> [M 0.107 Gb] Alloc WF ( 0.097)
<13s> [WF] Performing Wave-Functions I/O
<13s> [FFT-HF/Rho] Mesh size: 75 75 12
<13s> [M 0.119 Gb] Alloc wf_disk ( 0.011)
<13s> [M 0.108 Gb] Free wf_disk ( 0.011)
<13s> EXS | | [000%] --(E) --(X)
<18s> EXS |######### | [023%] 05s(E) 21s(X)
<23s> EXS |################### | [047%] 10s(E) 20s(X)
<28s> EXS |############################ | [071%] 15s(E) 21s(X)
<33s> EXS |###################################### | [095%] 20s(E) 20s(X)
<34s> EXS |########################################| [100%] 20s(E) 20s(X)
<34s> [xc] Functional Slater exchange(X)+Perdew & Zunger(C)
<34s> [xc] LIBXC used to calculate xc functional
<34s> [M 0.010 Gb] Free WF ( 0.097)
<35s> [06.01] HF occupations report
<35s> [07] Dyson equation: Newton solver
<35s> [07.01] G0W0 : the P(lasmon) P(ole) A(pproximation)
<36s> [M 0.198 Gb] Alloc WF ( 0.188)
<36s> [WF] Performing Wave-Functions I/O
<36s> [FFT-GW] Mesh size: 54 54 9
<36s> [M 0.209 Gb] Alloc wf_disk ( 0.011)
<37s> [M 0.198 Gb] Free wf_disk ( 0.011)
<37s> G0W0 PPA | | [000%] --(E) --(X)
<43s> G0W0 PPA |# | [002%] 06s(E) 04m-07s(X)
<49s> G0W0 PPA |## | [005%] 12s(E) 04m-05s(X)
[ERROR] STOP signal received while in :[07.01] G0W0 : the P(lasmon) P(ole) A(pproximation)
[ERROR][NetCDF] NetCDF: Start+count exceeds dimension bound[ERROR] STOP signal received while in :[07.01] G0W0 : the P(lasmon) P(ole) A(pproximation)
[ERROR][NetCDF] NetCDF: Start+count exceeds dimension bound[/code]
Here's an excerpt of my build-script:
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[...]
module load compiler/intel/14.0
module load mpi/openmpi/1.8-intel-14.0
module load numlib/mkl/11.1.4
module load lib/netcdf/4.4.2_fortran-openmpi-1.8-intel-14.0
./configure --enable-dp --enable-openmpi --enable-netcdf --enable-netcdf-LFS --with-blas-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-lapack-libs="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --prefix=${TARGET_DIR}/bin 2>&1 | tee ${LOG_DIR}/configure.out
make all 2>&1 | tee ${LOG_DIR}/make_all.out # approx. 24 min.
[...]Code: Select all
[...]
echo " "
echo "### initializing yambo db..."
# "Number of cores allocated to job: $MOAB_PROCCOUNT"
yambo
mpiexec -quiet -n ${MOAB_PROCCOUNT} yambo -F Inputs/02_QP_PPA_pure-mpi-q -J 02_QP_PPA_pure-mpi-q
[ "$?" -eq 0 ] && echo "all clean..." || echo "ERROR!"http://www.yambo-code.org/tutorials/Parallel/index.php
BTW: There's a dead-link here: [01] Initialization: 01_init (yambo -i -V RL)
ANY IDEAS WHAT I DID WRONG?
