installation error on HPC

[vasp-hpc]

I am trying to install vasp for HPC at university, and the attachment are the machines, make files, and errors we got.

[alexey.tal]

Hi,

Code: Select all

fpp: Command not found

This error indicates that you have not provided the paths to the required libraries and executables. If you have modules set up on your HPC facility you can load the Intel OneAPI module. Otherwise, you can find the path to the oneapi directory and source the environment variables:

Code: Select all

source /path/to/your/inteloneapi/installation/setvars.sh

[vasp-hpc]

We are on Centos-7.9, and we sourced the setvars.sh but still getting alot of errors; thanks
------------------------
[root@gpu-0-4 oneapi]# source /opt/intel/oneapi/setvars.sh

:: initializing oneAPI environment ...
-bash: BASH_VERSION = 4.2.46(2)-release
args: Using "$@" for setvars.sh arguments:
:: advisor -- latest
:: ccl -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: ipp -- latest
:: ippcp -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vtune -- latest
:: oneAPI environment initialized ::

[root@gpu-0-4 oneapi]#
[root@gpu-0-4 vasp.6.4.3]# make DEPS=1 -j8 all
if [ ! -d build/std ] ; then mkdir -p build/std ; fi
if [ ! -d build/gam ] ; then mkdir -p build/gam ; fi
if [ ! -d build/ncl ] ; then mkdir -p build/ncl ; fi
.
.
.
.
.
make -C parser -j1
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/std/parser'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make -C lib -j1
make libparser.a
make build_info
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/std/lib'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make libdmy.a
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/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&-D_OPENMP'\n" > build_info.inc
make[3]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/std/parser'
icpc -D YY_parse_DEBUG=1 -c sites.cpp -o sites.o
make[3]: icpc: Command not found
make[3]: *** [sites.o] Error 127
make[3]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/std/parser'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/std/parser'
make[1]: *** [parser] Error 2
make[1]: *** Waiting for unfinished jobs....
make[3]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/std/lib'
mpif90 -qopenmp -O1 -free -names lowercase -c -o preclib.o preclib.f90
printf " character(len=*), parameter :: link_line = '&\n&mpif90 &\n&-qmkl &\n&-Llib &\n&-ldmy &\n&-Lparser &\n&-lparser &\n&-lstdc++ &\n&-L/path/to/your/scalapack/installation/lib &\n&-lscalapack'\n" >> build_info.inc
printf " character(len=*), parameter :: fc = '&\n&mpif90 &\n&-qopenmp'\n" >> build_info.inc
printf " character(len=*), parameter :: fcl = '&\n&mpif90 &\n&-qmkl'\n" >> build_info.inc
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/gam'
make[1]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/gam'
make -C build/gam VERSION=gam all
printf " character(len=*), parameter :: fflags = '&\n&-assume &\n&byterecl &\n&-w &\n&-xHOST'\n" >> build_info.inc
printf " character(len=*), parameter :: llibs = '&\n&-lstdc++ &\n&-L/path/to/your/scalapack/installation/lib &\n&-lscalapack'\n" >> build_info.inc
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/ncl'
make[1]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/gam'
rsync -ru ../../src/lib .
make[1]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/ncl'
make -C build/ncl VERSION=ncl all
rsync -ru ../../src/parser .
rsync -u ../../src/*.F ../../src/*.inc .
printf " character(len=*), parameter :: incs = '&\n&-I/opt/intel/oneapi/mkl/2024.2/include/fftw'\n" >> build_info.inc
cp makefile.include parser
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/std'
cp makefile.include lib
gfortran: error: lowercase: No such file or directory
gfortran: error: unrecognized command line option ‘-qopenmp’
gfortran: error: unrecognized command line option ‘-names’
make[3]: *** [preclib.o] Error 1
make[3]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/std/lib'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/std/lib'
make[1]: *** [lib] Error 2
make[1]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/std'
make: *** [std] Error 2
make: *** Waiting for unfinished jobs....
make[1]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/ncl'
rsync -ru ../../src/lib .
rsync -ru ../../src/parser .
make -C parser -j1
make build_info
rsync -u ../../src/*.F ../../src/*.inc .
make -C lib -j1
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/gam/lib'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/gam/parser'
make libdmy.a
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/gam'
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&-D_OPENMP'\n" > build_info.inc
make libparser.a
cp makefile.include parser
make[3]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/gam/parser'
icpc -D YY_parse_DEBUG=1 -c sites.cpp -o sites.o
make[3]: icpc: Command not found
make[3]: *** [sites.o] Error 127
make[3]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/gam/parser'
printf " character(len=*), parameter :: link_line = '&\n&mpif90 &\n&-qmkl &\n&-Llib &\n&-ldmy &\n&-Lparser &\n&-lparser &\n&-lstdc++ &\n&-L/path/to/your/scalapack/installation/lib &\n&-lscalapack'\n" >> build_info.inc
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/gam/parser'
make[1]: *** [parser] Error 2
make[1]: *** Waiting for unfinished jobs....
make[3]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/gam/lib'
mpif90 -qopenmp -O1 -free -names lowercase -c -o preclib.o preclib.f90
make -C parser -j1
cp makefile.include lib
printf " character(len=*), parameter :: fc = '&\n&mpif90 &\n&-qopenmp'\n" >> build_info.inc
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/ncl/parser'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make build_info
make libparser.a
make -C lib -j1
printf " character(len=*), parameter :: fcl = '&\n&mpif90 &\n&-qmkl'\n" >> build_info.inc
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/ncl/lib'
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make libdmy.a
make[3]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/ncl/parser'
icpc -D YY_parse_DEBUG=1 -c sites.cpp -o sites.o
make[3]: icpc: Command not found
make[3]: *** [sites.o] Error 127
make[3]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/ncl/parser'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/ncl/parser'
make[1]: *** [parser] Error 2
make[1]: *** Waiting for unfinished jobs....
printf " character(len=*), parameter :: fflags = '&\n&-assume &\n&byterecl &\n&-w &\n&-xHOST'\n" >> build_info.inc
make[3]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/ncl/lib'
mpif90 -qopenmp -O1 -free -names lowercase -c -o preclib.o preclib.f90
printf " character(len=*), parameter :: llibs = '&\n&-lstdc++ &\n&-L/path/to/your/scalapack/installation/lib &\n&-lscalapack'\n" >> build_info.inc
make[2]: Entering directory `/home/hudao/appenv/vasp.6.4.3/build/ncl'
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&-D_OPENMP'\n" > build_info.inc
printf " character(len=*), parameter :: incs = '&\n&-I/opt/intel/oneapi/mkl/2024.2/include/fftw'\n" >> build_info.inc
printf " character(len=*), parameter :: link_line = '&\n&mpif90 &\n&-qmkl &\n&-Llib &\n&-ldmy &\n&-Lparser &\n&-lparser &\n&-lstdc++ &\n&-L/path/to/your/scalapack/installation/lib &\n&-lscalapack'\n" >> build_info.inc
printf " character(len=*), parameter :: fc = '&\n&mpif90 &\n&-qopenmp'\n" >> build_info.inc
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/gam'
printf " character(len=*), parameter :: fcl = '&\n&mpif90 &\n&-qmkl'\n" >> build_info.inc
gfortran: error: lowercase: No such file or directory
printf " character(len=*), parameter :: fflags = '&\n&-assume &\n&byterecl &\n&-w &\n&-xHOST'\n" >> build_info.inc
gfortran: error: unrecognized command line option ‘-qopenmp’
gfortran: error: unrecognized command line option ‘-names’
make[3]: *** [preclib.o] Error 1
make[3]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/gam/lib'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/gam/lib'
make[1]: *** [lib] Error 2
make[1]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/gam'
make: *** [gam] Error 2
printf " character(len=*), parameter :: llibs = '&\n&-lstdc++ &\n&-L/path/to/your/scalapack/installation/lib &\n&-lscalapack'\n" >> build_info.inc
printf " character(len=*), parameter :: incs = '&\n&-I/opt/intel/oneapi/mkl/2024.2/include/fftw'\n" >> build_info.inc
gfortran: error: lowercase: No such file or directory
gfortran: error: unrecognized command line option ‘-qopenmp’
gfortran: error: unrecognized command line option ‘-names’
make[3]: *** [preclib.o] Error 1
make[3]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/ncl/lib'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/ncl/lib'
make[1]: *** [lib] Error 2
make[2]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/ncl'
make[1]: Leaving directory `/home/hudao/appenv/vasp.6.4.3/build/ncl'
make: *** [ncl] Error 2
[root@gpu-0-4 vasp.6.4.3]#

[alexey.tal]

icpc: Command not found

This error indicates that the necessary tools are not found in your environment. Could you try compiling VASP with arch/makefile.include.intel ?
Also, could you please provide the output of the following command on the machine where you are trying to compile the code and attach the makefile.include you are using?

Code: Select all

echo $LD_LIBRARY_PATH

[vasp-hpc]

[root@gpu-0-4 oneapi]# source /opt/intel/oneapi/setvars.sh

:: initializing oneAPI environment ...
-bash: BASH_VERSION = 4.2.46(2)-release
args: Using "$@" for setvars.sh arguments:
:: advisor -- latest
:: ccl -- latest
:: compiler -- latest
:: dal -- latest
:: debugger -- latest
:: dev-utilities -- latest
:: dnnl -- latest
:: dpcpp-ct -- latest
:: dpl -- latest
:: ipp -- latest
:: ippcp -- latest
:: mkl -- latest
:: mpi -- latest
:: tbb -- latest
:: vtune -- latest
:: oneAPI environment initialized ::

[root@gpu-0-4 oneapi]#
[root@gpu-0-4 oneapi]# which mpirun
/opt/intel/oneapi/mpi/2021.13/bin/mpirun
[root@gpu-0-4 oneapi]# echo $LD_LIBRARY_PATH
/opt/intel/oneapi/tbb/2021.13/env/../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.13/opt/mpi/libfabric/lib:/opt/intel/oneapi/mpi/2021.13/lib:/opt/intel/oneapi/mkl/2024.2/lib:/opt/intel/oneapi/ippcp/2021.12/lib/:/opt/intel/oneapi/ipp/2021.12/lib:/opt/intel/oneapi/dpl/2022.6/lib:/opt/intel/oneapi/dnnl/2024.2/lib:/opt/intel/oneapi/debugger/2024.2/opt/debugger/lib:/opt/intel/oneapi/dal/2024.5/lib:/opt/intel/oneapi/compiler/2024.2/opt/compiler/lib:/opt/intel/oneapi/compiler/2024.2/lib:/opt/intel/oneapi/ccl/2021.13/lib/
[root@gpu-0-4 oneapi]#

thanks

[alexey.tal]

Could you please attach your makefile.include?

Also, I see that your are using Intel OneAPI 2024.2, which is quite new, so you should use arch/makefile.include.oneapi

[vasp-hpc]

Just a note: when i tar off the file it took on a different user id and group; and not root....not sure if this matters:
[root@turingh1 appenv]# ls -lrt
drwxrwxr-x 8 1724400005 1724400005 152 Mar 19 02:20 vasp.6.4.3
-rw-r--r-- 1 root root 99369143 Jul 18 18:28 vasp.6.4.3.tgz
[root@turingh1 appenv]#

Should I change ownership and groups to root?
[root@turingh1 vasp.6.4.3]# ls -lrt
total 28
drwxrwxr-x 2 1724400005 1724400005 4096 Mar 19 02:17 arch
drwxr-xr-x 5 1724400005 1724400005 214 Mar 19 02:19 testsuite
-rw-rw-r-- 1 1724400005 1724400005 575 Mar 19 02:20 README.md
-rw-rw-r-- 1 1724400005 1724400005 919 Mar 19 02:20 makefile
drwxrwxr-x 2 1724400005 1724400005 10 Mar 19 02:20 bin
drwxrwxr-x 2 1724400005 1724400005 10 Mar 19 02:20 build
drwxr-xr-x 5 1724400005 1724400005 12288 Mar 19 02:21 src
drwxr-xr-x 2 1724400005 1724400005 200 Mar 19 02:24 tools
[root@turingh1 vasp.6.4.3]# cd arch

=================
i used the stocked file: arch/makefile.include.intel_ompi_mkl_omp

[root@turingh1 vasp.6.4.3]# cat makefile.include-too-new
# 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 \
-D_OPENMP

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

FC = mpif90 -qopenmp
FCL = mpif90

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 ?= -xHOST
FFLAGS += $(VASP_TARGET_CPU)

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

# Use a separate scaLAPACK installation (optional but recommended in combination with OpenMPI)
# Comment out the two lines below if you want to use scaLAPACK from MKL instead
SCALAPACK_ROOT ?= /path/to/your/scalapack/installation
LLIBS += -L${SCALAPACK_ROOT}/lib -lscalapack

# HDF5-support (optional but strongly recommended)
#CPP_OPTIONS+= -DVASP_HDF5
#HDF5_ROOT ?= /path/to/your/hdf5/installation
#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

# For the fftlib library (hardly any benefit in combination with MKL's FFTs)
#CPP_OPTION += -Dsysv
#FCL = mpif90 fftlib.o -qmkl
#CXX_FFTLIB = icpc -qopenmp -std=c++11 -DFFTLIB_USE_MKL -DFFTLIB_THREADSAFE
#INCS_FFTLIB = -I./include -I$(MKLROOT)/include/fftw
#LIBS += fftlib
[root@turingh1 vasp.6.4.3]#

[alexey.tal]

Should I change ownership and groups to root?

I don't think that your issue is caused by the ownership.

Since you are using a new version of the Intel OneAPI compiler you should compile VASP with arch/makefile.include.oneapi, which uses the LLVM-based compilers of Intel. The older version of Intel OneAPI provided both classic and LLVM-based compilers, but the classic one was supposed to be deprecated at some point and I suspect that in your version it is no longer present.
That would explain the fact that you sourced setvars.sh, but still get this error

Code: Select all

 icpc: Command not found

[vasp-hpc]

Now trying with makefile.include.oneapi; please see attached logs.
thanks

[vasp-hpc]

Now trying Build VASP with Intel® oneAPI Base and HPC Toolkit
(unable to build "libfftw3xf_intel.a" )
ref: https://www.intel.com/content/www/us/en ... ilers.html

source /opt/intel/oneapi/setvars.sh
cd /opt/intel/oneapi/mkl/2024.2/share/mkl/interfaces/fftw3xf
make libintel64

[root@gpu-0-4 fftw3xf]# make libintel64
make -f makefile lib _IA=intel64
make[1]: Entering directory `/opt/intel/oneapi/mkl/2024.2/share/mkl/interfaces/fftw3xf'
mkdir -p ./obj_intel
icx -Wall -Werror -I/opt/intel/oneapi/mkl/2024.2/include -I/opt/intel/oneapi/mkl/2024.2/inclrfaces/fftw3xf/wrappers/fftw_alignment_of.c -o obj_intel/fftw_alignment_of.o
/opt/intel/oneapi/compiler/2024.2/bin/compiler/clang: /lib64/libc.so.6: version `GLIBC_2.18' n/compiler/clang)
/opt/intel/oneapi/compiler/2024.2/bin/compiler/clang: /lib64/libc.so.6: version `GLIBC_2.28' n/compiler/clang)
make[1]: *** [obj_intel/fftw_alignment_of.o] Error 1
make[1]: Leaving directory `/opt/intel/oneapi/mkl/2024.2/share/mkl/interfaces/fftw3xf'
make: *** [libintel64] Error 2
[root@gpu-0-4 fftw3xf]#