Compile VASP 6.4.3 issue

Questions regarding the compilation of VASP on various platforms: hardware, compilers and libraries, etc.


Moderators: Global Moderator, Moderator

Post Reply
Message
Author
sang-woo_joo1
Newbie
Newbie
Posts: 14
Joined: Fri Jan 19, 2024 4:25 am

Compile VASP 6.4.3 issue

#1 Post by sang-woo_joo1 » Tue Jul 09, 2024 7:12 am

Dear all,

I have issue when I compile the vasp, I used the lasted oneAPI base tool kit and HDF5

The error say:
precated [-Wdeprecated]
icpx -D YY_parse_DEBUG=1 -c lex.yy.c -o lex.yy.o
icpx -D YY_parse_DEBUG=1 -c lex.yy.c -o lex.yy.o
icpx: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
icpx: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
icpx -D YY_parse_DEBUG=1 -c locproj.tab.c -o locproj.tab.o
icpx: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
icpx -D YY_parse_DEBUG=1 -c locproj.tab.c -o locproj.tab.o
icpx -D YY_parse_DEBUG=1 -c locproj.tab.c -o locproj.tab.o
icpx: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
icpx: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
icpx -D YY_parse_DEBUG=1 -c yywrap.c -o yywrap.o
icpx: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
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
icpx -D YY_parse_DEBUG=1 -c yywrap.c -o yywrap.o
make[3]: Leaving directory '/home/ssu/NguynSourceCode/vasp.6.4.3/build/ncl/parser'
make[2]: Leaving directory '/home/ssu/NguynSourceCode/vasp.6.4.3/build/ncl/parser'
make[1]: Leaving directory '/home/ssu/NguynSourceCode/vasp.6.4.3/build/ncl'
make: *** [makefile:17: ncl] Error 2
make: *** Waiting for unfinished jobs....
icpx -D YY_parse_DEBUG=1 -c yywrap.c -o yywrap.o
icpx: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
icpx: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
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/ssu/NguynSourceCode/vasp.6.4.3/build/std/parser'
make[2]: Leaving directory '/home/ssu/NguynSourceCode/vasp.6.4.3/build/std/parser'
make[1]: Leaving directory '/home/ssu/NguynSourceCode/vasp.6.4.3/build/std'
make: *** [makefile:17: std] Error 2
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/ssu/NguynSourceCode/vasp.6.4.3/build/gam/parser'
make[2]: Leaving directory '/home/ssu/NguynSourceCode/vasp.6.4.3/build/gam/parser'
make[1]: Leaving directory '/home/ssu/NguynSourceCode/vasp.6.4.3/build/gam'
make: *** [makefile:17: gam] Error 2
Thank you in advance.

This is a makefile.include file
# 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 = icx
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)

OBJECTS_LIB = linpack_double.o

# For the parser library
CXX_PARS = icpx
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 ?= /opt/intel/oneapi/mkl/2024.2
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 ?= /opt/intel/oneapi/mkl/2024.2
LLIBS += -L${SCALAPACK_ROOT}/lib -lscalapack

# HDF5-support (optional but strongly recommended)
CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT ?= /home/ssu/HDF5_Intel/hdf5-1.14.4-2/build
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

alexey.tal
Global Moderator
Global Moderator
Posts: 310
Joined: Mon Sep 13, 2021 12:45 pm

Re: Compile VASP 6.4.3 issue

#2 Post by alexey.tal » Tue Jul 09, 2024 12:29 pm

Please provide further information according to the Forum Posting Guidelines. In order to assist you, I need at least the makefile.include and the full output of the make/compilation process that contains the error messages.

sang-woo_joo1
Newbie
Newbie
Posts: 14
Joined: Fri Jan 19, 2024 4:25 am

Re: Compile VASP 6.4.3 issue

#3 Post by sang-woo_joo1 » Wed Jul 10, 2024 1:41 am

Here is the error for vasp.

Thank you.
You do not have the required permissions to view the files attached to this post.

alexey.tal
Global Moderator
Global Moderator
Posts: 310
Joined: Mon Sep 13, 2021 12:45 pm

Re: Compile VASP 6.4.3 issue

#4 Post by alexey.tal » Wed Jul 10, 2024 11:25 am

Thank you for providing the files.
I see that you get errors from gfortran:
gfortran: error: unrecognized command-line option -qopenmp; did you mean -fopenmp?

If you are compiling VASP with Intel OneAPI, so you should change mpif90 to mpiifort. But I highly recommend you using the makefile.include from the arch/ directory, where most of the correct commands and variables are already provided.

sang-woo_joo1
Newbie
Newbie
Posts: 14
Joined: Fri Jan 19, 2024 4:25 am

Re: Compile VASP 6.4.3 issue

#5 Post by sang-woo_joo1 » Thu Jul 11, 2024 9:21 am

I have changed and this said this error:

ld: warning: libintlc.so.5, needed by /opt/intel/oneapi/compiler/2024.2/lib/libimf.so, not found (try using -rpath or -rpath-link)
You do not have the required permissions to view the files attached to this post.

alexey.tal
Global Moderator
Global Moderator
Posts: 310
Joined: Mon Sep 13, 2021 12:45 pm

Re: Compile VASP 6.4.3 issue

#6 Post by alexey.tal » Thu Jul 11, 2024 11:26 am

It is a warning, not an error. Does the code run after the compilation? Did you see if this library is present in you oneapi directory? Also, I see that you are using a different makefile.include from the one we provide in the arch directory. Is there a reason for it? Did the compilation not work for you with arch/makefile.include.intel_omp?

sang-woo_joo1
Newbie
Newbie
Posts: 14
Joined: Fri Jan 19, 2024 4:25 am

Re: Compile VASP 6.4.3 issue

#7 Post by sang-woo_joo1 » Fri Jul 12, 2024 9:11 am

It has run the code and then when I "make test" but it said error. I has linked the /opt/intel/oneapi/compiler/2024.2/lib in the bashrc.

Any ideas for this.

Thank you for replying to me.

alexey.tal
Global Moderator
Global Moderator
Posts: 310
Joined: Mon Sep 13, 2021 12:45 pm

Re: Compile VASP 6.4.3 issue

#8 Post by alexey.tal » Fri Jul 12, 2024 9:18 am

Do you mean that some of the tests failed?
Could you please attach the full error message?

sang-woo_joo1
Newbie
Newbie
Posts: 14
Joined: Fri Jan 19, 2024 4:25 am

Re: Compile VASP 6.4.3 issue

#9 Post by sang-woo_joo1 » Mon Jul 15, 2024 7:23 am

This is the error file and makefile.include.

I have write this in the bashrc:
source /opt/intel/oneapi/setvars.sh
You do not have the required permissions to view the files attached to this post.

alexey.tal
Global Moderator
Global Moderator
Posts: 310
Joined: Mon Sep 13, 2021 12:45 pm

Re: Compile VASP 6.4.3 issue

#10 Post by alexey.tal » Mon Jul 15, 2024 9:43 am

Code: Select all

error while loading shared libraries: libmkl_intel_lp64.so.2: cannot open shared object file
This error suggests that the path to the mkl library is not set up correctly.

Could you please provide the output for the following command?

Code: Select all

echo $LD_LIBRARY_PATH

sang-woo_joo1
Newbie
Newbie
Posts: 14
Joined: Fri Jan 19, 2024 4:25 am

Re: Compile VASP 6.4.3 issue

#11 Post by sang-woo_joo1 » Wed Jul 17, 2024 9:21 am

I have compile the vasp successfully ( I added path in /.bashrc ) and when I make test it is error like this, thank you for helping me.
You do not have the required permissions to view the files attached to this post.

alexey.tal
Global Moderator
Global Moderator
Posts: 310
Joined: Mon Sep 13, 2021 12:45 pm

Re: Compile VASP 6.4.3 issue

#12 Post by alexey.tal » Wed Jul 17, 2024 9:53 am

These tests might be failing because of the stack size limit.
Could you run

Code: Select all

ulimit -s
and if it returns a number add the following line in your .bashrc

Code: Select all

ulimit -s unlimited
and then try to run the tests again?

sang-woo_joo1
Newbie
Newbie
Posts: 14
Joined: Fri Jan 19, 2024 4:25 am

Re: Compile VASP 6.4.3 issue

#13 Post by sang-woo_joo1 » Thu Jul 18, 2024 9:11 am

When I tried this command ulimit -s it said: unlimited and I write this ulimit -s unlimited in bashrc, it still error like the same.

alexey.tal
Global Moderator
Global Moderator
Posts: 310
Joined: Mon Sep 13, 2021 12:45 pm

Re: Compile VASP 6.4.3 issue

#14 Post by alexey.tal » Thu Jul 18, 2024 9:48 am

I just noticed that according to your typescript file you are actually running VASP 6.4.1, not VASP 6.4.3. Was it your intention? Do you have the same problem with VASP 6.4.3?

Post Reply