Installation of VASP 6.2 - Tests failed

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frank_niessen
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Installation of VASP 6.2 - Tests failed

#1 Post by frank_niessen » Thu Mar 11, 2021 11:39 am

Hi,

I just installed VASP 6.2 on a HPC cluster and the installation succeeded. However, I got an error report in the end of the test that the following tests failed "bulk_InP_SOC_G0W0_sym bulk_InP_SOC_G0W0_sym_RPR bulk_SiO2_LOPTICS bulk_SiO2_LOPTICS_RPR bulk_SiO2_LPEAD bulk_SiO2_LPEAD_RPR".

How can I figure out what is wrong with the installation? Attached are my makefile.include and the testsuite.log output.
Thank you for your help

Frank
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Re: Installation of VASP 6.2 - Tests failed

#2 Post by merzuk.kaltak » Thu Mar 11, 2021 1:05 pm

Please use one of the makefile.include.linux_intel* makefiles for intel in the arch path of the tar ball.
If you still have failed tests, please let us know. Also let us know which OS you are using.

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Re: Installation of VASP 6.2 - Tests failed

#3 Post by frank_niessen » Thu Mar 11, 2021 4:19 pm

The cluster runs on "Scientific Linux 7.7 (Nitrogen)". I got the make file adapted by the technical cluster support for VASP 5 and I tried to adapt it to version 6.

I just tried installing using the makefile.include.linux_intel file and got this error:



if [ ! -d build/std ] ; then mkdir build/std ; fi;
cp src/makefile src/.objects src/makedeps.awk makefile.include build/std ;
make -C build/std VERSION=std cleandependencies -j1
make[1]: Entering directory `/zhome/4e/1/74988/vasp_6_2_0/build/std'
rm -f .depend
make[1]: Leaving directory `/zhome/4e/1/74988/vasp_6_2_0/build/std'
make -C build/std VERSION=std all
make[1]: Entering directory `/zhome/4e/1/74988/vasp_6_2_0/build/std'
rsync -ru ../../src/lib .
cp makefile.include lib
make -C lib -j1
make[2]: Entering directory `/zhome/4e/1/74988/vasp_6_2_0/build/std/lib'
make libdmy.a
make[3]: Entering directory `/zhome/4e/1/74988/vasp_6_2_0/build/std/lib'
make[3]: `libdmy.a' is up to date.
make[3]: Leaving directory `/zhome/4e/1/74988/vasp_6_2_0/build/std/lib'
make[2]: Leaving directory `/zhome/4e/1/74988/vasp_6_2_0/build/std/lib'
rsync -ru ../../src/parser .
cp makefile.include parser
make -C parser -j1
make[2]: Entering directory `/zhome/4e/1/74988/vasp_6_2_0/build/std/parser'
make libparser.a
make[3]: Entering directory `/zhome/4e/1/74988/vasp_6_2_0/build/std/parser'
make[3]: `libparser.a' is up to date.
make[3]: Leaving directory `/zhome/4e/1/74988/vasp_6_2_0/build/std/parser'
make[2]: Leaving directory `/zhome/4e/1/74988/vasp_6_2_0/build/std/parser'
rsync -u ../../src/*.F ../../src/*.inc .
rm -f vasp ; make vasp ; cp vasp ../../bin/vasp_std
make[2]: Entering directory `/zhome/4e/1/74988/vasp_6_2_0/build/std'
mpiifort -mkl=sequential -o vasp c2f_interface.o nccl2for.o simd.o base.o profiling.o string.o tutor.o version.o vhdf5_base.o incar_reader.o reader_base.o openmp.o openacc_struct.o mpi.o mpi_shmem.o mathtools.o hamil_struct.o radial_struct.o pseudo_struct.o mgrid_struct.o wave_struct.o nl_struct.o mkpoints_struct.o poscar_struct.o afqmc_struct.o phonon_struct.o fock_glb.o chi_glb.o smart_allocate.o xml.o extpot_glb.o constant.o vdwforcefield_glb.o jacobi.o main_mpi.o openacc.o scala.o asa.o lattice.o poscar.o ini.o mgrid.o setex_struct.o xclib.o vdw_nl.o xclib_grad.o setex.o radial.o pseudo.o gridq.o ebs.o symlib.o mkpoints.o wave.o wave_mpi.o wave_high.o bext.o spinsym.o symmetry.o lattlib.o random.o nonl.o nonlr.o nonl_high.o dfast.o choleski2.o mix.o hamil.o xcgrad.o xcspin.o potex1.o potex2.o constrmag.o cl_shift.o relativistic.o LDApU.o paw_base.o metagga.o egrad.o pawsym.o pawfock.o pawlhf.o diis.o rhfatm.o hyperfine.o fock_ace.o paw.o mkpoints_full.o charge.o Lebedev-Laikov.o stockholder.o dipol.o solvation.o scpc.o pot.o tet.o dos.o elf.o hamil_rot.o chain.o dyna.o fileio.o vhdf5.o sphpro.o us.o core_rel.o aedens.o wavpre.o wavpre_noio.o broyden.o dynbr.o reader.o writer.o xml_writer.o brent.o stufak.o opergrid.o stepver.o chgloc.o fast_aug.o fock_multipole.o fock.o fock_dbl.o fock_frc.o mkpoints_change.o subrot_cluster.o sym_grad.o mymath.o npt_dynamics.o subdftd3.o subdftd4.o internals.o dynconstr.o dimer_heyden.o dvvtrajectory.o vdwforcefield.o nmr.o pead.o k-proj.o subrot.o subrot_scf.o paircorrection.o rpa_force.o ml_interface.o force.o pwlhf.o gw_model.o optreal.o steep.o rmm-diis.o davidson.o david_inner.o root_find.o lcao_bare.o locproj.o electron_common.o electron.o rot.o electron_all.o shm.o pardens.o optics.o constr_cell_relax.o stm.o finite_diff.o elpol.o hamil_lr.o rmm-diis_lr.o subrot_lr.o lr_helper.o hamil_lrf.o elinear_response.o ilinear_response.o linear_optics.o setlocalpp.o wannier.o electron_OEP.o electron_lhf.o twoelectron4o.o gauss_quad.o m_unirnk.o minimax_ini.o minimax_dependence.o minimax_functions1D.o minimax_functions2D.o minimax_struct.o minimax_varpro.o minimax.o mlwf.o ratpol.o pade_fit.o screened_2e.o wave_cacher.o crpa.o chi_base.o wpot.o local_field.o ump2.o ump2kpar.o fcidump.o ump2no.o bse_te.o bse.o time_propagation.o acfdt.o afqmc.o rpax.o chi.o acfdt_GG.o dmft.o GG_base.o greens_orbital.o lt_mp2.o rnd_orb_mp2.o greens_real_space.o chi_GG.o chi_super.o sydmat.o rmm-diis_mlr.o linear_response_NMR.o wannier_interpol.o wave_interpolate.o linear_response.o auger.o dmatrix.o phonon.o wannier_mats.o elphon.o core_con_mat.o embed.o extpot.o fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o main.o -Llib -ldmy -Lparser -lparser /opt/intel/2020update1/compilers_and_libraries_2020.1.217/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a -lmkl_blacs_intelmpi_lp64 -lstdc++
make[2]: Leaving directory `/zhome/4e/1/74988/vasp_6_2_0/build/std'
make[1]: Leaving directory `/zhome/4e/1/74988/vasp_6_2_0/build/std'

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Re: Installation of VASP 6.2 - Tests failed

#4 Post by merzuk.kaltak » Fri Mar 12, 2021 10:36 am

Dear Frank,

your post doesn't show any errors.

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Re: Installation of VASP 6.2 - Tests failed

#5 Post by frank_niessen » Fri Mar 12, 2021 11:39 am

You are right, that was embarrassing :)

Anyways, VASP did compile and I ran the test again. This time I got even more errors:

==================================================================
SUMMARY:
==================================================================
The following tests failed, please check the output file manually:
andersen_nve andersen_nve_constrain_fixed andersen_nve_constrain_fixed_RPR andersen_nve_RPR andersen_nvt andersen_nvt_fixed andersen_nvt_RPR bulk_InP_SOC_DFT_ISYM=2 bulk_InP_SOC_DFT_ISYM=2_RPR bulk_InP_SOC_DFT_ISYM=3 bulk_InP_SOC_DFT_ISYM=3_RPR bulk_InP_SOC_G0W0_sym bulk_InP_SOC_G0W0_sym_RPR bulk_InP_SOC_PBE0_nosym bulk_InP_SOC_PBE0_nosym_RPR bulk_InP_SOC_PBE0_sym bulk_InP_SOC_PBE0_sym_RPR bulk_SiO2_LOPTICS bulk_SiO2_LOPTICS_RPR bulk_SiO2_LPEAD bulk_SiO2_LPEAD_RPR NiOsLDAU=2_x NiOsLDAU=2_x_RPR NiOsLDAU=2_y NiOsLDAU=2_y_RPR NiOsLDAU=2_z NiOsLDAU=2_z_RPR Tl_x Tl_x_RPR Tl_y Tl_y_RPR Tl_z Tl_z_RPR
make[1]: *** [test] Error 1
make[1]: Leaving directory `/zhome/4e/1/74988/vasp_6_2_0/testsuite'
make: *** [test] Error 2

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Re: Installation of VASP 6.2 - Tests failed

#6 Post by frank_niessen » Thu Mar 18, 2021 1:22 pm

I compiled VASP on a different cluster, this time I only got the following errors:

andersen_nve_constrain_fixed andersen_nve_constrain_fixed_RPR andersen_nvt_fixed

is this a reason for concern?

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Re: Installation of VASP 6.2 - Tests failed

#7 Post by frank_niessen » Mon Mar 29, 2021 6:53 am

Hi, I would like to point out that this issue is still not solved, I would appreciate a reply.

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Re: Installation of VASP 6.2 - Tests failed

#8 Post by merzuk.kaltak » Mon Mar 29, 2021 8:07 am

Hello Frank,

Can you post more information about which modules you are loading and if the corresponding modules correspond to one of the supported toolchains?

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Re: Installation of VASP 6.2 - Tests failed

#9 Post by frank_niessen » Mon Mar 29, 2021 8:41 am

Hi,

I am using the Intel 2020b toolchain, described on this link: https://docs.easybuild.io/en/master/Com ... -toolchain

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Re: Installation of VASP 6.2 - Tests failed

#10 Post by frank_niessen » Mon Mar 29, 2021 8:45 am

in more detail:

Currently Loaded Modules:
1) GCCcore/10.2.0 6) UCX/1.9.0-GCCcore-10.2.0
2) zlib/1.2.11-GCCcore-10.2.0 7) impi/2019.9.304-iccifort-2020.4.304
3) binutils/2.35-GCCcore-10.2.0 8) iimpi/2020b
4) iccifort/2020.4.304 9) imkl/2020.4.304-iimpi-2020b
5) numactl/2.0.13-GCCcore-10.2.0 10) intel/2020b

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Re: Installation of VASP 6.2 - Tests failed

#11 Post by roger_amos1 » Tue Mar 30, 2021 2:28 am

If your jobs of category andersen...fixed.., are still failing, and if you have -xHost in your makefile.include, then take it out.
That's what I had to do

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Re: Installation of VASP 6.2 - Tests failed

#12 Post by frank_niessen » Wed Mar 31, 2021 10:59 am

Dear Roger,

thank for your advice.
When I replace

FFLAGS = -assume byterecl -w -xHOST

with

FFLAGS = -assume byterecl -w -xHOST

I seem to run into the error:

fortran.c(68): catastrophic error: cannot open source file "cuda_runtime.h"
#include <cuda_runtime.h>
^

Code: Select all

compilation aborted for fortran.c (code 4)
make[3]: *** [obj/x86_64/release/fortran.c.o] Error 4
make[3]: Leaving directory `/home/mek/frannie/VASP_6_2_0/build/gpu/CUDA'
make[2]: *** [release] Error 2
make[2]: Leaving directory `/home/mek/frannie/VASP_6_2_0/build/gpu/CUDA'
make[1]: *** [CUDA] Error 2
make[1]: Leaving directory `/home/mek/frannie/VASP_6_2_0/build/gpu'
make: *** [gpu] Error 2
Have you experienced anything like this?

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Re: Installation of VASP 6.2 - Tests failed

#13 Post by frank_niessen » Mon Jun 07, 2021 1:27 pm

So just to revive the topic,

I have been trying to compile VASP again and again with different setups, and the best result I could achieve sofar was:
The following tests failed, please check the output file manually:
bulk_InP_SOC_G0W0_sym bulk_InP_SOC_G0W0_sym_RPR bulk_SiO2_LOPTICS bulk_SiO2_LOPTICS_RPR bulk_SiO2_LPEAD bulk_SiO2_LPEAD_RPR
Here I used the intel/2020.0.166 toolchain with mpi support and cuda 10.0.

I attached the makefile.include (identical to the makefile.include.linux_intel), the testsuite.log file as well as the outputs of a SOC and an LOPTICS test.
I would be happy for any suggestions to figure out why the tests fail.

Thanks and best wishes
Frank
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Re: Installation of VASP 6.2 - Tests failed

#14 Post by martin.schlipf » Tue Jun 08, 2021 6:54 am

Just to be sure: Do you want to compile with GPU support? If yes, please note that the CUDA port of VASP is deprecated and you should use the OpenACC one instead.

Regarding your failing tests: We can clearly see some segmentation faults in the testsuite.log file. While this can point to a bug in the code another likely alternative is that the setup you run does not have sufficient memory.

Unfortunately we can offer no support to resolve this issue if you are using the CUDA version of VASP, because it is no longer maintained. Please try to use the OpenACC version instead and if the problem persists we will try to assist you.

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Re: Installation of VASP 6.2 - Tests failed

#15 Post by frank_niessen » Tue Jun 08, 2021 7:04 am

Great. I am actually not interested in GPU support, I want to run VASP on an HPC with standard CPU's. But since the CUDA compiler is part of the standard make-file (wiki/index.php/Makefile.include.linux_intel) I thought I would need to load the CUDA module. How would I go about excluding GPU support during compiling? (I apologize for potentially trivial questions)

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