Error libsvml.so

[Sherif_Yehia1]

Dear experts

I am getting this "libsvml.so" library error when I compile vasp although this lib in intel at
/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin/libsvml.so
I tried to put file with its location on /etc/ld.so.conf.d/

I keep getting the same following error

ld: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/intel64/../../bin/intel64/../../lib/icx-lto.so: error loading plugin: libsvml.so: cannot open shared object file: No such file or directory
make[2]: *** [makefile:132: vasp] Error 1
1-My operating system red hat 8.7
2-Intel compiler Oneapi
3-Please see my makefile.include

# Precompiler options
CPP_OPTIONS= -DHOST=\"LinuxIFC\"\
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Duse_bse_te \
-Dtbdyn \
-Dfock_dblbuf

CPP = fpp -f_com=no -free -w0 $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)

FC = ifort
FCL = ifort -qmkl=sequential

FREE = -free -names lowercase

FFLAGS = -assume byterecl -w -march=core-avx2
OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0

MKL_PATH = $ /opt/intel/oneapi/mkl/2023.0.0/lib/intel64
BLAS =
LAPACK =
"makefile.include" 53L, 1159C

Thanks in advance for your constant help
Best regards

[jonathan_lahnsteiner2]

Dear Sherif_Yehia1,

What version of vasp are you compiling? The latest vasp versions
have a folder arch in the main directory. From there you could
copy the makefile.include_intel to your main directory. In this makefile.include
you have to adapt the following lines

Code: Select all

# Intel MKL (FFTW, BLAS, LAPACK, and scaLAPACK)
# (Note: for Intel Parallel Studio's MKL use -mkl instead of -qmkl)
FCL        += -qmkl=sequential
MKLROOT    ?= /path/to/your/mkl/installation

So you have to fill in the path to your mkl installation.
Maybe also check if your LD_LIBRARY_PATH is set properly. This
can be set with the mkl setvars.sh script, which is in your mkl main folder.
A description of setvars.sh can be found here:
https://www.intel.com/content/www/us/en ... macos.html

I hope this helps. Otherwise contact us again.

All the best Jonathan

[Sherif_Yehia1]

Dear Jonathan

Thank you very much for the quick reply
I followed you advise to make sure that the intel setting is correct

[sherifyehia@192 ~]$ su
Password:
(base) [root@192 sherifyehia]# env | grep SETVARS_COMPLETED
SETVARS_COMPLETED=1

my vasp version is 6.3.2
Please see my makefile.include

# Default precompiler options
CPP_OPTIONS = -DHOST=\"LinuxIFC\" \
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Duse_bse_te \
-Dtbdyn \
-Dfock_dblbuf

CPP = fpp -f_com=no -free -w0 $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)

FC = mpiifort
FCL = mpiifort

FREE = -free -names lowercase

FFLAGS = -assume byterecl -w

OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0

OBJECTS = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o
OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o

# For what used to be vasp.5.lib
CPP_LIB = $(CPP)
FC_LIB = $(FC)
CC_LIB = icc
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)

OBJECTS_LIB = linpack_double.o

# For the parser library
CXX_PARS = icpc
LLIBS = -lstdc++

##
## Customize as of this point! Of course you may change the preceding
## part of this file as well if you like, but it should rarely be
## necessary ...
##

# When compiling on the target machine itself, change this to the
# relevant target when cross-compiling for another architecture
VASP_TARGET_CPU ?= -march=core-avx2
FFLAGS += $(VASP_TARGET_CPU)

# Intel MKL (FFTW, BLAS, LAPACK, and scaLAPACK)
# (Note: for Intel Parallel Studio's MKL use -mkl instead of -qmkl)
FCL += -qmkl=sequential
MKLROOT ?= /opt/intel/oneapi/mkl/
LLIBS += -L$(MKLROOT)/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
INCS =-I$(MKLROOT)/include/fftw

# HDF5-support (optional but strongly recommended)
#CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT ?= /home/sherifyehia/Desktop/Codes/hdf5-1.13.2
LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran
INCS += -I$(HDF5_ROOT)/include

# For the VASP-2-Wannier90 interface (optional)
#CPP_OPTIONS += -DVASP2WANNIER90
#WANNIER90_ROOT ?= /path/to/your/wannier90/installation
#LLIBS += -L$(WANNIER90_ROOT)/lib -lwannier


I got the error

ld: /opt/intel/oneapi/compiler/2023.0.0/linux/bin/intel64/../../bin/intel64/../../lib/icx-lto.so: error loading plugin: libirng.so: cannot open shared object file: No such file or directory
make[2]: *** [makefile:132: vasp] Error 1
make[2]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.3.2/build/std'
cp: cannot stat 'vasp': No such file or directory
make[1]: *** [makefile:129: all] Error 1
make[1]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.3.2/build/std'
make: *** [makefile:17: std] Error 2

The lib is there

[sherifyehia@192 ~]$ su
Password:
(base) [root@192 sherifyehia]# env | grep SETVARS_COMPLETED
SETVARS_COMPLETED=1
(base) [root@192 sherifyehia]# su
(base) [root@192 sherifyehia]# find /opt/ -name "libirng.so"
/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/ia32_lin/libirng.so
/opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin/libirng.so
/opt/intel/oneapi/clck/2021.7.2/lib_common/intel64/libirng.so

Thank you
Best Regards,
Sherif

[jonathan_lahnsteiner2]

Dear Sherif_Yehia1,

I tried now with the setup you are referring to. I don't get any linking
issues with intel oneAPI and intel oneHPC toolkit 2023.0 as you are reporting them.
My suspicion is now that maybe there went something wrong when
installing the intel tool kits.
I would recommend you to the following step by step procedure
First you have to install the intel Base for the one api:

Code: Select all

wget https://registrationcenter-download.intel.com/akdlm/irc_nas/19079/l_BaseKit_p_2023.0.0.25537_offline.sh
bash l_BaseKit_p_2023.0.0.25537_offline.sh

And make the default installation. The next step is to install the intel HPC tool-kits.

Code: Select all

wget https://registrationcenter-download.intel.com/akdlm/irc_nas/19084/l_HPCKit_p_2023.0.0.25400_offline.sh
bash ./l_HPCKit_p_2023.0.0.25400_offline.sh

Also make a default installation for this package. Then you have to source the setvars.sh file as:

Code: Select all

source ${HOME}/intel/oneapi/setvars.sh

Then go to your vasp base folder and copy

Code: Select all

cp arch/makefile.include.intel makefile.include

And now without changing anything in the makefile.include do a

Code: Select all

make DEPS=1 -j std

Then the vasp_std should compile without any issues. Could you please try this step by step procedure.
And if it does not work please send the whole compiler output, at least the whole error output.
And could you also send the output of

Code: Select all

echo $MKLROOT
echo $LD_LIBRARY_PATH

I hope this is of help to you.

All the best Jonathan

[Sherif_Yehia1]

Dear jonathan_lahnsteiner

As you advised I started step by step
Yes everything is perfect your magic method solved almost all the problem the makefile.include is the same.
I got the executable files

[sherifyehia@localhost bin]$ ls
vasp_gam vasp_ncl vasp_std

Thank you for all the help and efforts

Once I opened the CPP option i.e CPP_OPTIONS+= -DVASP_HDF5

I have the following errors

(base) [root@localhost vasp.6.4.0]# make veryclean
rm -rf build/std
rm -rf build/gam
rm -rf build/ncl
(base) [root@localhost vasp.6.4.0]# make all
if [ ! -d build/std ] ; then mkdir -p build/std ; fi
cp src/makefile src/.objects src/makedeps.awk makefile.include build/std
make -C build/std VERSION=std check
make[1]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
exit 0
make[1]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
make -C build/std VERSION=std cleandependencies -j1
make[1]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
rm -f .depend
make[1]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
make -C build/std VERSION=std all
make[1]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
rsync -ru ../../src/lib .
cp makefile.include lib
make -C lib -j1
make[2]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std/lib'
make libdmy.a
make[3]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std/lib'
fpp -f_com=no -free -w0 preclib.F preclib.f90
mpiifort -O1 -free -names lowercase -c -o preclib.o preclib.f90
icc -O -c -o timing_.o timing_.c
icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
icc -O -c -o derrf_.o derrf_.c
icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
icc -O -c -o dclock_.o dclock_.c
icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
fpp -f_com=no -free -w0 diolib.F diolib.f90
mpiifort -O1 -free -names lowercase -c -o diolib.o diolib.f90
fpp -f_com=no -free -w0 dlexlib.F dlexlib.f90
mpiifort -O1 -free -names lowercase -c -o dlexlib.o dlexlib.f90
fpp -f_com=no -free -w0 drdatab.F drdatab.f90
mpiifort -O1 -free -names lowercase -c -o drdatab.o drdatab.f90
mpiifort -O1 -c linpack_double.f
rm -f libdmy.a
ar vq libdmy.a preclib.o timing_.o derrf_.o dclock_.o diolib.o dlexlib.o drdatab.o linpack_double.o
ar: creating libdmy.a
a - preclib.o
a - timing_.o
a - derrf_.o
a - dclock_.o
a - diolib.o
a - dlexlib.o
a - drdatab.o
a - linpack_double.o
make[3]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std/lib'
make[2]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std/lib'
rsync -ru ../../src/parser .
cp makefile.include parser
make -C parser -j1
make[2]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std/parser'
make libparser.a
make[3]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std/parser'
icpc -D YY_parse_DEBUG=1 -c sites.cpp -o sites.o
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
icpc -D YY_parse_DEBUG=1 -c functions.cpp -o functions.o
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
icpc -D YY_parse_DEBUG=1 -c radial.cpp -o radial.o
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
icpc -D YY_parse_DEBUG=1 -c basis.cpp -o basis.o
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
icpc -D YY_parse_DEBUG=1 -c lex.yy.c -o lex.yy.o
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
icpc -D YY_parse_DEBUG=1 -c locproj.tab.c -o locproj.tab.o
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
icpc -D YY_parse_DEBUG=1 -c yywrap.c -o yywrap.o
icpc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
rm -f libparser.a
ar vq libparser.a sites.o functions.o radial.o basis.o lex.yy.o locproj.tab.o yywrap.o locproj.tab.h
ar: creating libparser.a
a - sites.o
a - functions.o
a - radial.o
a - basis.o
a - lex.yy.o
a - locproj.tab.o
a - yywrap.o
a - locproj.tab.h
make[3]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std/parser'
make[2]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std/parser'
rsync -u ../../src/*.F ../../src/*.inc .
make build_info
make[2]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
printf " character(len=*), parameter :: cpp_options = '&\n&-DHOST=\"LinuxIFC\" &\n&-DMPI &\n&-DMPI_BLOCK=8000 &\n&-Duse_collective &\n&-DscaLAPACK &\n&-DCACHE_SIZE=4000 &\n&-Davoidalloc &\n&-Dvasp6 &\n&-Duse_bse_te &\n&-Dtbdyn &\n&-Dfock_dblbuf &\n&-DVASP_HDF5'\n" > build_info.inc
printf " character(len=*), parameter :: link_line = '&\n&mpiifort &\n&-qmkl=sequential &\n&-Llib &\n&-ldmy &\n&-Lparser &\n&-lparser &\n&-lstdc++ &\n&-L/opt/intel/oneapi/mkl/2023.0.0/lib/intel64 &\n&-lmkl_scalapack_lp64 &\n&-lmkl_blacs_intelmpi_lp64 &\n&-L/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/lib &\n&-lhdf5_fortran'\n" >> build_info.inc
printf " character(len=*), parameter :: fc = '&\n&mpiifort'\n" >> build_info.inc
printf " character(len=*), parameter :: fcl = '&\n&mpiifort &\n&-qmkl=sequential'\n" >> build_info.inc
printf " character(len=*), parameter :: fflags = '&\n&-assume &\n&byterecl &\n&-w &\n&-march=core-avx2'\n" >> build_info.inc
printf " character(len=*), parameter :: llibs = '&\n&-lstdc++ &\n&-L/opt/intel/oneapi/mkl/2023.0.0/lib/intel64 &\n&-lmkl_scalapack_lp64 &\n&-lmkl_blacs_intelmpi_lp64 &\n&-L/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/lib &\n&-lhdf5_fortran'\n" >> build_info.inc
printf " character(len=*), parameter :: incs = '&\n&-I/opt/intel/oneapi/mkl/2023.0.0/include/fftw &\n&-I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include'\n" >> build_info.inc
make[2]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
rm -f vasp ; make vasp ; cp vasp ../../bin/vasp_std
make[2]: Entering directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
fpp -f_com=no -free -w0 c2f_interface.F c2f_interface.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c c2f_interface.f90
fpp -f_com=no -free -w0 nccl2for.F nccl2for.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c nccl2for.f90
fpp -f_com=no -free -w0 simd.F simd.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c simd.f90
fpp -f_com=no -free -w0 base.F base.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c base.f90
fpp -f_com=no -free -w0 profiling.F profiling.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c profiling.f90
fpp -f_com=no -free -w0 string.F string.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c string.f90
fpp -f_com=no -free -w0 tutor.F tutor.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c tutor.f90
fpp -f_com=no -free -w0 version.F version.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c version.f90
fpp -f_com=no -free -w0 build_info.F build_info.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c build_info.f90
fpp -f_com=no -free -w0 command_line.F command_line.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c command_line.f90
fpp -f_com=no -free -w0 vhdf5_base.F vhdf5_base.f90 -DHOST=\"LinuxIFC\" -DMPI -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK -DCACHE_SIZE=4000 -Davoidalloc -Dvasp6 -Duse_bse_te -Dtbdyn -Dfock_dblbuf -DVASP_HDF5 -DNGZhalf
mpiifort -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/home/sherifyehia/Desktop/Codes/hdf5-1.13.2/hdf5/include -c vhdf5_base.f90
vhdf5_base.F(7): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [HDF5]
use hdf5
------^
vhdf5_base.F(37): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5intermediategroup_id
----------^
vhdf5_base.F(38): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5infileid
----------^
vhdf5_base.F(39): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outfileid
----------^
vhdf5_base.F(40): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5wavefileid
----------^
vhdf5_base.F(41): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5ininputgroup_id
----------^
vhdf5_base.F(42): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outinputgroup_id
----------^
vhdf5_base.F(43): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outoriginalgroup_id
----------^
vhdf5_base.F(58): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T) :: create_inter_prop
----------^
vhdf5_base.F(169): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(175): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T) :: dspace, dset
------------^
vhdf5_base.F(176): error #6683: A kind type parameter must be a compile-time constant. [HSIZE_T]
integer(HSIZE_T) :: maxdims(rank)
------------^
vhdf5_base.F(177): error #6683: A kind type parameter must be a compile-time constant. [HSIZE_T]
integer(HSIZE_T) :: my_dims(rank)
------------^
vhdf5_base.F(225): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(239): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(253): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(268): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(284): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(295): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(337): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: fileid
------------^
vhdf5_base.F(365): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(367): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(378): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(391): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(393): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(408): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(410): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(431): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(447): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent[sherifyehia@localhost bin]$ ls /usr/local/hdf5/lib/
libhdf5.a libhdf5hl_fortran.a libhdf5_hl.so.300
libhdf5_fortran.a libhdf5hl_fortran.la libhdf5_hl.so.300.0.2
libhdf5_fortran.la libhdf5_hl_fortran.so libhdf5.la
libhdf5_fortran.so libhdf5hl_fortran.so libhdf5.settings
libhdf5_fortran.so.300 libhdf5hl_fortran.so.300 libhdf5.so
libhdf5_fortran.so.300.0.2 libhdf5hl_fortran.so.300.0.2 libhdf5.so.302
libhdf5_hl.a libhdf5_hl.la libhdf5.so.302.0.0
libhdf5_hl_fortran.a libhdf5_hl.so
(in) :: locid
------------^
vhdf5_base.F(472): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.f90(2830): catastrophic error: Too many errors, exiting
compilation aborted for vhdf5_base.f90 (code 1)
make[2]: *** [makefile:167: vhdf5_base.o] Error 1
make[2]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
cp: cannot stat 'vasp': No such file or directory
make[1]: *** [makefile:129: all] Error 1
make[1]: Leaving directory '/home/sherifyehia/Desktop/vasp.6.4.0/build/std'
make: *** [makefile:17: std] Error 2
(base) [root@localhost vasp.6.4.0]#

I am not sure but I must be be doing something wrong with hdf5

P.S.
[sherifyehia@localhost bin]$ ls /usr/local/hdf5/lib/
libhdf5.a libhdf5hl_fortran.a libhdf5_hl.so.300
libhdf5_fortran.a libhdf5hl_fortran.la libhdf5_hl.so.300.0.2
libhdf5_fortran.la libhdf5_hl_fortran.so libhdf5.la
libhdf5_fortran.so libhdf5hl_fortran.so libhdf5.settings
libhdf5_fortran.so.300 libhdf5hl_fortran.so.300 libhdf5.so
libhdf5_fortran.so.300.0.2 libhdf5hl_fortran.so.300.0.2 libhdf5.so.302
libhdf5_hl.a libhdf5_hl.la libhdf5.so.302.0.0
libhdf5_hl_fortran.a libhdf5_hl.so

I hope you can point my mistakes

Thank you
Sherif

[Sherif_Yehia1]

Dear jonathan_lahnsteiner

Continuing to my previous post I used the following code to download mistakenly HDF5_VERSION=1.14.0
I know that the recommend one for vasp only version 1.13 is the tested one (sorry for the not intention run ).

source /opt/intel/oneapi/setvars.sh intel64
export HDF5_VERSION=1.14.0
export STRIP_PATCH=$(echo $HDF5_VERSION | awk -F. '{ print $1"."$2 }')
export CC=icx
export CXX=icpx
export FC=ifort
export CFLAGS='-march=core-avx2'
export CXXFLAGS='-march=core-avx2'
export FCFLAGS='-march=core-avx2'
export LDFLAGS=-L/opt/intel/oneapi/mkl/2023.0.0/lib/intel64
wget https://support.hdfgroup.org/ftp/HDF5/r ... ION.tar.gz
tar -zxvf hdf5-$HDF5_VERSION.tar.gz
cd hdf5-$HDF5_VERSION
./configure --enable-fortran --enable-cxx
make
make check
make install
exit

Because Luckily it work in my case this encourage me to run the test. I got another error


fatal: your current branch 'master' does not have any commits yet
VASP TESTSUITE SHA:

Reference files have been generated with 4 MPI ranks.
Note that tests might fail if an other number of ranks is used!

Executables and additional INCAR tags used for this test:

VASP_TESTSUITE_EXE_STD="mpirun -np 4 /home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_std"
VASP_TESTSUITE_EXE_NCL="mpirun -np 4 /home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_ncl"
VASP_TESTSUITE_EXE_GAM="mpirun -np 4 /home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam"
VASP_TESTSUITE_INCAR_PREPEND=""
VASP_TESTSUITE_REFERENCE=""
VASP_TESTSUITE_SKIP_HYB=""
VASP_TESTSUITE_SKIP_NCL=""
VASP_TESTSUITE_SKIP_SOC=""
VASP_TESTSUITE_SKIP_MD=""
VASP_TESTSUITE_SKIP_TBMD=""
VASP_TESTSUITE_SKIP_RPA=""
VASP_TESTSUITE_SKIP_GW=""
VASP_TESTSUITE_SKIP_ACFDT=""
VASP_TESTSUITE_SKIP_CRPA=""
VASP_TESTSUITE_SKIP_BSE=""
VASP_TESTSUITE_SKIP_NOSYM=""
VASP_TESTSUITE_SKIP_VASP6=""
VASP_TESTSUITE_SKIP_GAMMA=""
VASP_TESTSUITE_SKIP_VASP45="Y"
VASP_TESTSUITE_SKIP_VASP46=""
VASP_TESTSUITE_SKIP_LREAL=""
VASP_TESTSUITE_SKIP_LRESP=""
VASP_TESTSUITE_SKIP_PEAD=""
VASP_TESTSUITE_SKIP_NCORE1=""
VASP_TESTSUITE_SKIP_WAN90=""
VASP_TESTSUITE_SKIP_KOPT=""
VASP_TESTSUITE_SKIP_ML=""
VASP_TESTSUITE_SKIP_LIBXC=""
VASP_TESTSUITE_RUN_HYB=""
VASP_TESTSUITE_RUN_NCL=""
VASP_TESTSUITE_RUN_SOC=""
VASP_TESTSUITE_RUN_MD=""
VASP_TESTSUITE_RUN_TBMD=""
VASP_TESTSUITE_RUN_RPA=""
VASP_TESTSUITE_RUN_GW=""
VASP_TESTSUITE_RUN_ACFDT=""
VASP_TESTSUITE_RUN_CRPA=""
VASP_TESTSUITE_RUN_BSE=""
VASP_TESTSUITE_RUN_NOSYM=""
VASP_TESTSUITE_RUN_VASP6=""
VASP_TESTSUITE_RUN_GAMMA=""
VASP_TESTSUITE_RUN_LREAL=""
VASP_TESTSUITE_RUN_LRESP=""
VASP_TESTSUITE_RUN_PEAD=""
VASP_TESTSUITE_RUN_NCORE1=""
VASP_TESTSUITE_RUN_WAN90=""
VASP_TESTSUITE_RUN_KOPT=""
VASP_TESTSUITE_RUN_ML=""
VASP_TESTSUITE_RUN_LIBXC=""
VASP_TESTSUITE_RUN_FAST="Y"

Executed at: 12_25_03/04/23
==================================================================

------------------------------------------------------------------

CASE: andersen_nve
------------------------------------------------------------------
CASE: andersen_nve
entering run_recipe andersen_nve
andersen_nve step STD
------------------------------------------------------------------
andersen_nve step STD
entering run_vasp_g
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
exiting run_vasp_g
exiting run_recipe andersen_nve
./runtest: line 471: OUTCAR: No such file or directory
ERROR: the test yields different results for the energies, please check
-----------------------------------------------------------------------
paste: energy_outcar: No such file or directory
ERROR: compare_numbertable can't find file energy_outcar
./runtest: line 593: OUTCAR: No such file or directory
ERROR: the test yields different results for the forces, please check
---------------------------------------------------------------------
cat: force: No such file or directory
ERROR: compare_numbertable can't find file force
grep: OUTCAR: No such file or directory
ERROR: the stress tensor is different, please check
---------------------------------------------------
---------------------------------------------------------------------------
WARNING: Number of rows and/or columns in files stress and stress.ref disagree.
Please check! Continuing using the smaller number of columns and/or rows.
---------------------------------------------------------------------------


CASE: andersen_nve_constrain_fixed
------------------------------------------------------------------
CASE: andersen_nve_constrain_fixed
entering run_recipe andersen_nve_constrain_fixed
andersen_nve_constrain_fixed step STD
------------------------------------------------------------------
andersen_nve_constrain_fixed step STD
entering run_vasp_g
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
exiting run_vasp_g
exiting run_recipe andersen_nve_constrain_fixed
./runtest: line 471: OUTCAR: No such file or directory
ERROR: the test yields different results for the energies, please check
-----------------------------------------------------------------------
paste: energy_outcar: No such file or directory
ERROR: compare_numbertable can't find file energy_outcar
./runtest: line 593: OUTCAR: No such file or directory
ERROR: the test yields different results for the forces, please check
---------------------------------------------------------------------
cat: force: No such file or directory
ERROR: compare_numbertable can't find file force
grep: OUTCAR: No such file or directory
ERROR: the stress tensor is different, please check
---------------------------------------------------
---------------------------------------------------------------------------
WARNING: Number of rows and/or columns in files stress and stress.ref disagree.
Please check! Continuing using the smaller number of columns and/or rows.
---------------------------------------------------------------------------


CASE: andersen_nve_constrain_fixed_RPR
------------------------------------------------------------------
CASE: andersen_nve_constrain_fixed_RPR
entering run_recipe andersen_nve_constrain_fixed_RPR
andersen_nve_constrain_fixed_RPR step STD
------------------------------------------------------------------
andersen_nve_constrain_fixed_RPR step STD
entering run_vasp_g
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory
/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory

I hope you can direct me in case moved to the wrong direction
Thank you very much
Best Regards,
Sherif

[jonathan_lahnsteiner2]

Dear Sherif_Yehia,

You are receiving the error message

Code: Select all

/home/sherifyehia/Desktop/vasp.6.4.0/testsuite/../bin/vasp_gam: error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file: No such file or directory

This is again related to the shared libraries of intel one api. The message tells you that something from
the mkl library can not be found. Did you run

Code: Select all

source ${HOME}/intel/oneapi/setvars.sh

before executing the vasp code?
The following error messages that you receive are follow up errors of not setting the correct library paths.
I hope this is of help.

All the best Jonathan

[Sherif_Yehia1]

Dear Jonathan

Thank you very much for all the constant help

As per your advice Now I ran the vasp hopefully no error.

I had to run all attached commends in my terminal even though in my .bashrc. I thought to put it in my reply if you agree to be for other users benefit .As well I put the success run (I hope it is OK) for other with your permission.

If you think I am in the right track I will go ahead and start to learn that genius software.

Thank you very much
Waiting your guidance and permission
Sherif