error in compiling lammps interface with vasp6.5 install

[suojiang_zhang1]

dear:
I try to compile lammps to interface with vasp6.5 vaspml. before I sucessfully install vasp6.5
with:

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CPP_OPTIONS += -Dlibvaspml
CPP_OPTIONS += -DVASPML_USE_CBLAS
CPP_OPTIONS += -DVASPML_USE_MKL
#CPP_OPTIONS += -DVASPML_DEBUG_LEVEL=3
CXX_ML      = mpiicpc  -cxx=icpx
CXXFLAGS_ML = -O3 -std=c++17 -Wall
INCLUDE_ML  =

I refer to the link wiki/index.php/Running_machine-learned_ ... _in_LAMMPS
but When I "make mpi", I met errors as follows:

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s<char>, std::allocator<char> > > > >::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
TagTranslator.cpp:(.text._ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixERS9_[_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixERS9_]+0x166): undefined reference to `_intel_fast_memcpy'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:105: ../lmp_mpi] Error 1
make[1]: Leaving directory '/public/software/lammps/src/Obj_mpi'
make: *** [Makefile:401: mpi] Error 2

[andreas.singraber]

Hello!

Could you please post all information related to the build process? This would include:

• VASP makefile.include

• Modified LAMMPS Makefile.mpi

• Toolchain used, i.e. which compiler and version did you use? If you use a module system which did you load? For example, post the output of

  Code: Select all

  mpiicpc -cxx=icpx --version

Thank you!

All the best,
Andreas Singraber

[suojiang_zhang1]

the make.include looks like:

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# Default precompiler options

CPP_OPTIONS = -DHOST=\"LinuxIFC\" \
              -DMPI -DMPI_BLOCK=8000 -Duse_collective \
              -DscaLAPACK \
              -DCACHE_SIZE=4000 \
              -Davoidalloc \
              -Dvasp6 \
              -Dtbdyn \
              -Dfock_dblbuf

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

FC          = mpiifort -fc=ifx
FCL         = mpiifort -fc=ifx

FREE        = -free -names lowercase

FFLAGS      = -assume byterecl -w

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

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

# HDF5-support (optional but strongly recommended, and mandatory for some features)
#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 machine learning library vaspml (experimental)
CPP_OPTIONS += -Dlibvaspml
CPP_OPTIONS += -DVASPML_USE_CBLAS
CPP_OPTIONS += -DVASPML_USE_MKL
#CPP_OPTIONS += -DVASPML_DEBUG_LEVEL=3
CXX_ML      = mpiicpc -cxx=icpx
CXXFLAGS_ML = -O3 -std=c++17 -Wall
INCLUDE_ML  =

the Makefile.mpi looks like:

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# mpi = MPI with its default compiler

SHELL = /bin/sh

# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler

CC =		mpiicpc
CCFLAGS =	 -g -O3 -std=c++17 
SHFLAGS =	-fPIC
DEPFLAGS =	-M

LINK =		mpicx
LINKFLAGS =	 -g -O3 -std=c++17 
LIB =           

SIZE =		size

ARCHIVE =	ar
ARFLAGS =	-rc
SHLIBFLAGS =	-shared -rdynamic

the errors look like:

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mpiicpc -g -O3 -std=c++17  main.o        -L. -llammps_mpi      -L../../lib/vasp/vaspml/lib/ -lvaspml  -ldl  -o ../lmp_mpi
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.
../../lib/vasp/vaspml/lib//libvaspml.a(KernelPolynomial.o): In function `vaspml::KernelPolynomial::computeDerivativeKernel(std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, double const*, double const*, unsigned long const&, unsigned long const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
KernelPolynomial.cpp:(.text+0x32f0): undefined reference to `cblas_dgemm'
KernelPolynomial.cpp:(.text+0x3389): undefined reference to `cblas_dgemv'
KernelPolynomial.cpp:(.text+0x35ba): undefined reference to `cblas_daxpy'

[andreas.singraber]

Hello!

Thank you for the files! The errors in your posts do not match, it seems you changed the makefiles in the meantime, right?

Anyway, I think there are two separate issues in your build process:

1. Do not mix Intel oneAPI Compiler and Intel Compiler Classic. It seems you have access to the newer oneAPI compiler, hence I would recommend to stick to this one in all your makefiles. Here is an overview of the different compiler executable names:

   Code: Select all

   Intel Compiler Classic
   ######################
   Language | Compiler | MPI wrapper compiler
   ---------|----------|---------------------
   C        | icc      | mpiicc
   C++      | icpc     | mpiicpc
   Fortran  | ifort    | mpiifort
   
   Intel oneAPI Compiler
   #####################
   Language | Compiler | MPI wrapper compiler
   ---------|----------|---------------------------------------------
   C        | icx      | mpiicc -cc=icx     OR mpiicx  (if available)
   C++      | icpx     | mpiicpc -cxx=icpx  OR mpiicpx (if available)
   Fortran  | ifx      | mpiifort -fx=ifx   OR mpiifx  (if available)
   
   

   For example, with the Intel oneAPI compilers you should use this in your files (if the short versions are not available use the -cc,-cxx,-fx versions from the table above):

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   makefile.include:
   -----------------
   FC          = mpiifx
   FCL         = mpiifx
   CXX_PARS    = icpx
   CXX_ML      = mpiicpx
   

   and

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   Makefile.mpi:
   -------------
   CC =		mpiicpx
   LINK =		mpiicpx
   

2. You forgot to link to the BLAS and LAPACK libraries when linking the LAMMPS executable. This should be simple to fix by adding the MKL flag in the LAMMPS makefile:

   Code: Select all

   Makefile.mpi:
   -------------
   LINKFLAGS =	 -g -O3 -std=c++17 -qmkl=sequential
   

Can you try to update your makefiles accordingly and please report back if this resolves the issue? Thank you!

Best,
Andreas Singraber

[suojiang_zhang1]

thanks.
Now I try to compile the lammps from git clone https://github.com/vasp-dev/lammps.
I sucessfully compile vasp and got the vaspml by oneapi2024

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FC          = mpiifx -fc=ifx
FCL         = mpiifx -fc=ifx
CXX_PARS    = icpx
for ml:
CPP_OPTIONS += -Dlibvaspml
CPP_OPTIONS += -DVASPML_USE_CBLAS
CPP_OPTIONS += -DVASPML_USE_MKL
#CPP_OPTIONS += -DVASPML_DEBUG_LEVEL=3
CXX_ML      = mpicxx
CXXFLAGS_ML = -O3 -std=c++17 -pedantic-errors -Wall -Wextra
INCLUDE_ML  =

but I still fail to compile lammps:
in src/MAKE/Makefile.mpi

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CC =            mpicxx
CCFLAGS =       -g -O3  -std=c++17 -pedantic-errors -Wall -Wextra
SHFLAGS =       -fPIC
DEPFLAGS =      -M

LINK =          mpicxx
LINKFLAGS =     -g -O3 -std=c++17 -pedantic-errors -Wall -Wextra
LIB =

but errors look like when make mpi:

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mpicxx -g -O3 -std=c++17 -pedantic-errors -Wall -Wextra  main.o        -L. -llammps_mpi      -L../../lib/vasp/vaspml/lib/ -lvaspml  -ldl  -o ../lmp_mpi
../../lib/vasp/vaspml/lib//libvaspml.a(KernelPolynomial.o): In function `vaspml::KernelPolynomial::computeDerivativeKernel(std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, double const*, double const*, unsigned long const&, unsigned long const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const':
KernelPolynomial.cpp:(.text+0x405): undefined reference to `cblas_dgemm'
KernelPolynomial.cpp:(.text+0x56e): undefined reference to `cblas_dgemv'
KernelPolynomial.cpp:(.text+0xa0c): undefined reference to `cblas_daxpy'
../../lib/vasp/vaspml/lib//libvaspml.a(Kernel.o): In function `vaspml::Kernel::compute_kernelMatrix()':
Kernel.cpp:(.text+0x2002): undefined reference to `cblas_dgemm'
../../lib/vasp/vaspml/lib//libvaspml.a(DescriptorCollector.o): In function `vaspml::DescriptorCollector::computeNormSingleAtom(unsigned long)':
DescriptorCollector.cpp:(.text+0x37d): undefined reference to `cblas_dnrm2'
../../lib/vasp/vaspml/lib//libvaspml.a(DescriptorSHS2.o): In function `vaspml::DescriptorSHS2::computeForceTermsCPU(std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > const&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<double, std::allocator<double> >&) const':
DescriptorSHS2.cpp:(.text+0x1d13): undefined reference to `cblas_ddot'
DescriptorSHS2.cpp:(.text+0x1d6c): undefined reference to `cblas_ddot'
DescriptorSHS2.cpp:(.text+0x1dc6): undefined reference to `cblas_ddot'
DescriptorSHS2.cpp:(.text+0x1e8c): undefined reference to `cblas_ddot'
DescriptorSHS2.cpp:(.text+0x1ee4): undefined reference to `cblas_ddot'
../../lib/vasp/vaspml/lib//libvaspml.a(DescriptorSHS2.o):DescriptorSHS2.cpp:(.text+0x1f3b): more undefined references to `cblas_ddot' follow
../../lib/vasp/vaspml/lib//libvaspml.a(Predictor.o): In function `vaspml::Predictor::compute_energyArray(vaspml::Kernel const&, unsigned long, unsigned long, unsigned long, double)':
Predictor.cpp:(.text+0x1fb): undefined reference to `cblas_daxpy'
../../lib/vasp/vaspml/lib//libvaspml.a(Predictor.o): In function `vaspml::Predictor::updateEnergy(vaspml::Kernel const&)':
Predictor.cpp:(.text+0x1d4d): undefined reference to `cblas_daxpy'
Predictor.cpp:(.text+0x1d9d): undefined reference to `cblas_ddot'
../../lib/vasp/vaspml/lib//libvaspml.a(Predictor.o): In function `vaspml::Predictor::computeEnergyPerType(unsigned long, unsigned long)':
Predictor.cpp:(.text+0x261): undefined reference to `cblas_ddot'
../../lib/vasp/vaspml/lib//libvaspml.a(DescriptorSHS3ReducedLinElem.o): In function `vaspml::DescriptorSHS3ReducedLinElem::computeSHS3clnmNoElement()':
DescriptorSHS3ReducedLinElem.cpp:(.text+0xe1): undefined reference to `cblas_daxpy'
../../lib/vasp/vaspml/lib//libvaspml.a(DescriptorSHS3ReducedLinElem.o): In function `vaspml::DescriptorSHS3ReducedLinElem::computeSHS3(std::shared_ptr<vaspml::DescriptorSHS2> const&, vaspml::TypeMap const&)':
DescriptorSHS3ReducedLinElem.cpp:(.text+0x33dc): undefined reference to `cblas_daxpy'
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:105: ../lmp_mpi] Error 1
make[1]: Leaving directory '/public/software/lammps-dev/src/Obj_mpi'
make: *** [Makefile:401: mpi] Error 2

I will appreciate if you can help me improve the situation.
Thankyou

[andreas.singraber]

Hello!

Please read my instructions more carefully, you are still

• Potentially mixing different MPI wrappers (mpicxx, mpiifx) in both, VASP and LAMMPS makefiles. In particular, I never mentioned to use mpicxx which is not one of the standard Intel MPI wrapper compilers. However, if you can make sure that it is the same as mpiicpx it should still work.

• Also, you did not include the -qmkl=sequential flag in the LAMMPS Makefile.mpi as I asked you to do. Without it the linker will not find the BLAS/LAPACK routines and will give you the error you posted.

Please try to update your makefiles accordingly.

Best,
Andreas Singraber

[suojiang_zhang1]

Hi, thank for your conduction.
I recompiled the vasp using MPI wrappers mpiicpx and successfully compiled the lammps with interface with this vasp, =
After that, I trained a ML_FFN and copied the ML_FFN to ML_FF in the lammps to run the MD simulation. Compared with the last version, I have two questions:
1. when I ran the lammps, ERROR: This force field file does not support the fast prediction mode. Please perform a refit with ML_MODE = refit. but in the last version, I only do copy ML_FF, lammps can run. My question is why do refit and what is advance of ML_FF after refit?
2. In my lammps input file, if I set the constrain by fix, such as constrain the H by shake,
ERROR: Unrecognized fix style 'shake' is part of the RIGID package which is not enabled in this LAMMPS binary. But I could run lammps with the constrain by OPLS force field.