libmkl_intel_lp64.so: cannot open shared object file:

Questions regarding compilation of VASP on various platforms.

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libmkl_intel_lp64.so: cannot open shared object file:

Postby lineyarna » Tue Jun 17, 2014 11:34 pm

I?m compiling VASP.5.3 on Linux x86_64 using ifort 13.0

When I run the executable I get the following error:

VASP/src/vasp.5.3/vasp: error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory

But if I look at the linked files in the executable (ldd vasp) no files are missing:

/VASP/src/vasp.5.3 88% ldd vasp
linux-vdso.so.1 => (0x00007fff8a7ff000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x000000376f400000)
librt.so.1 => /lib64/librt.so.1 (0x000000376fc00000)
libmkl_intel_lp64.so => /nfs/stak/a1/rhel5apps64/intel/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_intel_lp64.so (0x00007ffdba9f7000)
libmkl_intel_thread.so => /nfs/stak/a1/rhel5apps64/intel/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_intel_thread.so (0x00007ffdb9a83000)
libmkl_core.so => /nfs/stak/a1/rhel5apps64/intel/composer_xe_2013.0.079/mkl/lib/intel64/libmkl_core.so (0x00007ffdb8887000)
libiomp5.so => /nfs/stak/a1/rhel5apps64/intel/composer_xe_2013.0.079/compiler/lib/intel64/libiomp5.so (0x00007ffdb858f000)
libm.so.6 => /lib64/libm.so.6 (0x000000376f000000)
libc.so.6 => /lib64/libc.so.6 (0x000000376e800000)
/lib64/ld-linux-x86-64.so.2 (0x000000376e400000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003773800000)
libdl.so.2 => /lib64/libdl.so.2 (0x000000376ec00000)

I appreciate any ideas ?
_______________________________
My Makefile looks like this:

# all CPP processed fortran files have the extension .f90
SUFFIX=.f90

#-----------------------------------------------------------------------
# fortran compiler and linker
#-----------------------------------------------------------------------
FC=ifort
#FC=mpif90
# fortran linker
FCL=$(FC)


#-----------------------------------------------------------------------
# whereis CPP ?? (I need CPP, can't use gcc with proper options)
# that's the location of gcc for SUSE 5.3
#
# CPP_ = /usr/lib/gcc-lib/i486-linux/2.7.2/cpp -P -C
#
# that's probably the right line for some Red Hat distribution:
#
# CPP_ = /usr/lib/gcc-lib/i386-redhat-linux/2.7.2.3/cpp -P -C
#
# SUSE X.X, maybe some Red Hat distributions:

CPP_ = ./preprocess <$*.F | /usr/bin/cpp -P -C -traditional >$*$(SUFFIX)

# this release should be fpp clean
# we now recommend fpp as preprocessor
# if this fails go back to cpp
#CPP_=fpp -f_com=no -free -w0 $*.F $*$(SUFFIX)
#-----------------------------------------------------------------------
# possible options for CPP:
# NGXhalf charge density reduced in X direction
# wNGXhalf gamma point only reduced in X direction
# avoidalloc avoid ALLOCATE if possible
# PGF90 work around some for some PGF90 / IFC bugs
# CACHE_SIZE 1000 for PII,PIII, 5000 for Athlon, 8000-12000 P4, PD
# RPROMU_DGEMV use DGEMV instead of DGEMM in RPRO (depends on used BLAS)
# RACCMU_DGEMV use DGEMV instead of DGEMM in RACC (depends on used BLAS)
# tbdyn MD package of Tomas Bucko
#-----------------------------------------------------------------------

CPP = $(CPP_) -DHOST=\"LinuxIFC\" \
-DCACHE_SIZE=12000 -DPGF90 -Davoidalloc \
# -DCACHE_SIZE=12000 -DPGF90 -Davoidalloc -DNGXhalf \
# -DRPROMU_DGEMV -DRACCMU_DGEMV

#-----------------------------------------------------------------------
# general fortran flags (there must a trailing blank on this line)
# byterecl is strictly required for ifc, since otherwise
# the WAVECAR file becomes huge
#-----------------------------------------------------------------------

FFLAGS = -FR -names lowercase -assume byterecl

#-----------------------------------------------------------------------
# optimization
# we have tested whether higher optimisation improves performance
# -axK SSE1 optimization, but also generate code executable on all mach.
# xK improves performance somewhat on XP, and a is required in order
# to run the code on older Athlons as well
# -xW SSE2 optimization
# -axW SSE2 optimization, but also generate code executable on all mach.
# -tpp6 P3 optimization
# -tpp7 P4 optimization
#-----------------------------------------------------------------------
# ifc.9.1, ifc.10.1 recommended
OFLAG=-O2 -ip

OFLAG_HIGH = $(OFLAG)
OBJ_HIGH =
OBJ_NOOPT =
DEBUG = -FR -O0
INLINE = $(OFLAG)

#-----------------------------------------------------------------------
# the following lines specify the position of BLAS and LAPACK
# we recommend to use mkl, that is simple and most likely
# fastest in Intel based machines
#-----------------------------------------------------------------------

# mkl path for ifc 11 compiler
#MKL_PATH=$(MKLROOT)/lib/em64t

# mkl path for ifc 12 compiler
MKL_PATH=$(MKLROOT)/lib/intel64

MKL_FFTW_PATH=$(MKLROOT)/interfaces/fftw3xf/

# BLAS
# setting -DRPROMU_DGEMV -DRACCMU_DGEMV in the CPP lines usually speeds up program execution

# BLAS= -Wl,--start-group $(MKL_PATH)/libmkl_intel_lp64.a $(MKL_PATH)/libmkl_intel_thread.a $(MKL_PATH)/libmkl_core.a -Wl,--end-group -lguide
# faster linking and available from at least version 11
#BLAS= -lguide -mkl

BLAS= -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_intel_thread.a -Wl,--end-group $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a -lpthread -mkl

# LAPACK, use vasp.5.lib/lapack_double

#LAPACK= ../vasp.5.lib/lapack_double.o

# LAPACK from mkl, usually faster and contains scaLAPACK as well

LAPACK= $(MKL_PATH)/libmkl_intel_lp64.a

# here a tricky version, link in libgoto and use mkl as a backup
# also needs a special line for LAPACK
# this is the best thing you can do on AMD based systems !!!!!!

#BLAS = -Wl,--start-group /opt/libs/libgoto/libgoto.so $(MKL_PATH)/libmkl_intel_thread.a $(MKL_PATH)/libmkl_core.a -Wl,--end-group -liomp5
#LAPACK= /opt/libs/libgoto/libgoto.so $(MKL_PATH)/libmkl_intel_lp64.a

#-----------------------------------------------------------------------

LIB = -L../vasp.5.lib -ldmy \
../vasp.5.lib/linpack_double.o $(LAPACK) \
$(BLAS)
# options for linking, nothing is required (usually)

#Link added
LINK =

#-----------------------------------------------------------------------
# fft libraries:
# VASP.5.2 can use fftw.3.1.X (http://www.fftw.org)
# since this version is faster on P4 machines, we recommend to use it
#-----------------------------------------------------------------------

FFT3D = fft3dfurth.o fft3dlib.o

# alternatively: fftw.3.1.X is slighly faster and should be used if available
#FFT3D = fftw3d.o fft3dlib.o /opt/libs/fftw-3.1.2/lib/libfftw3.a

# you may also try to use the fftw wrapper to mkl (but the path might vary a lot)
# it seems this is best for AMD based systems
#FFT3D = fftw3d.o fft3dlib.o $(MKL_FFTW_PATH)/libfftw3xf_intel.a
#INCS = -I$(MKLROOT)/include/fftw

#=======================================================================
# MPI section, uncomment the following lines until
# general rules and compile lines
# presently we recommend OPENMPI, since it seems to offer better
# performance than lam or mpich
#
# !!! Please do not send me any queries on how to install MPI, I will
# certainly not answer them !!!!
#=======================================================================
#-----------------------------------------------------------------------
# fortran linker for mpi
#-----------------------------------------------------------------------

FC=mpif90
FCL=$(FC)

#-----------------------------------------------------------------------
#-----------------------------------------------------------------------
# additional options for CPP in parallel version (see also above):
# NGZhalf charge density reduced in Z direction
# wNGZhalf gamma point only reduced in Z direction
# scaLAPACK use scaLAPACK (recommended if mkl is available)
# avoidalloc avoid ALLOCATE if possible
# PGF90 work around some for some PGF90 / IFC bugs
# CACHE_SIZE 1000 for PII,PIII, 5000 for Athlon, 8000-12000 P4, PD
# RPROMU_DGEMV use DGEMV instead of DGEMM in RPRO (depends on used BLAS)
# RACCMU_DGEMV use DGEMV instead of DGEMM in RACC (depends on used BLAS)
# tbdyn MD package of Tomas Bucko
#-----------------------------------------------------------------------

#-----------------------------------------------------------------------

CPP = $(CPP_) -DMPI -DHOST=\"LinuxIFC\" -DIFC \
-DCACHE_SIZE=16000 -DPGF90 -Davoidalloc \
# -DCACHE_SIZE=16000 -DPGF90 -Davoidalloc -DNGZhalf \
#-DCACHE_SIZE=4000 -DPGF90 -Davoidalloc -DNGZhalf \

-DMPI_BLOCK=8000 -Duse_collective

# -DscaLAPACK
## -DRPROMU_DGEMV -DRACCMU_DGEMV

#-----------------------------------------------------------------------
# location of SCALAPACK
# if you do not use SCALAPACK simply leave this section commented out
#-----------------------------------------------------------------------

# usually simplest link in mkl scaLAPACK
#BLACS= -lmkl_blacs_openmpi_lp64
#SCA= $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)

#-----------------------------------------------------------------------
# libraries
#-----------------------------------------------------------------------

LIB = -L../vasp.5.lib -ldmy \
../vasp.5.lib/linpack_double.o \
$(SCA) $(LAPACK) $(BLAS)

#-----------------------------------------------------------------------
# parallel FFT
#-----------------------------------------------------------------------

# FFT: fftmpi.o with fft3dlib of Juergen Furthmueller
FFT3D = fftmpi.o fftmpi_map.o fft3dfurth.o fft3dlib.o

# alternatively: fftw.3.1.X is slighly faster and should be used if available
#FFT3D = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o /opt/libs/fftw-3.1.2/lib/libfftw3.a

# you may also try to use the fftw wrapper to mkl (but the path might vary a lot)
# it seems this is best for AMD based systems
#FFT3D = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o $(MKL_FFTW_PATH)/libfftw3xf_intel.a
#INCS = -I$(MKLROOT)/include/fftw

#-----------------------------------------------------------------------
# general rules and compile lines
#-----------------------------------------------------------------------
Last edited by lineyarna on Tue Jun 17, 2014 11:34 pm, edited 1 time in total.
lineyarna
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libmkl_intel_lp64.so: cannot open shared object file:

Postby beck » Sun Jun 22, 2014 11:19 am

Did you run vasp on the same machine you did the "ldd" on? Or on some remote machine?
Last edited by beck on Sun Jun 22, 2014 11:19 am, edited 1 time in total.
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libmkl_intel_lp64.so: cannot open shared object file:

Postby lineyarna » Mon Jun 23, 2014 11:20 pm

I did the ldd on the same machine as I compiled. I managed to get this working for me but now I students get the same error when they try to run VASP
Last edited by lineyarna on Mon Jun 23, 2014 11:20 pm, edited 1 time in total.
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