CMake + ifort + hdf5
Paul Anton Letnes
We are currently trying to compile my fortran project with ifort while
linking to hdf5. I am failing at compiling with cmake, which I would
like to do, but I finally managed to compile with a single line in bash.
I attach my CMakeLists.txt (which works for gfortran) and the bash
command. If anyone can give some hints on how to link to hdf5
successfully, I would be very grateful!
As a side note, it appears that on the cluster I am trying to use, only
the h5pfc compiler is installed, not h5fc. I do not need mpi support, so
if it is possible to skip the mpi linking, I would be happy with that -
our end results are in the sub-GB region anyway. We are planning to
extend our program to use MPI, but we do not need to write from more
than one MPI process.
Regards,
Paul
PS:
I crossposted this post to the hdf5 mailing list as well.
+++++++++++++++++
Working command:
h5pfc -openmp Rayleigh2D_Modules/version.f90
Rayleigh2D_Modules/constants.f90
Rayleigh2D_Modules/derived_type_module.f90
Rayleigh2D_Modules/SFL_ISO_Fortran_Env.f90
Rayleigh2D_Modules/SFL_Logical_Units.f90
Rayleigh2D_Modules/Rayleigh2D_Utils.f90 Rayleigh2D_Modules/R_save.f90
Rayleigh2D_Modules/SFL_Error_Handling.f90
Rayleigh2D_Modules/SFL_Fourier.f90
Rayleigh2D_Modules/surface_util_module.f90
Rayleigh2D_Modules/surface_correlated_module.f90
Rayleigh2D_Modules/Rayleigh2D_Module.f90 FFT_Modules/fft_nms.f
FFT_Modules/fftpack.f90 Rayleigh2D.f90 -o Rayleigh2D -lmkl_intel_lp64
-lmkl_intel_thread -lmkl_core -lguide -I. -L.
$ h5pfc -show
mpif90 -fPIC
-I/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/include
-L/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_hl.a
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5.a -lz -lm
-lgpfs -Wl,-rpath -Wl,/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib
$ mpif90 -show
ifort -I/share/apps/modulessoftware/openmpi/openmpi-1.4.3-intel/include
-I/share/apps/modulessoftware/openmpi/openmpi-1.4.3-intel/lib
-L/share/apps/modulessoftware/openmpi/openmpi-1.4.3-intel/lib -lmpi_f90
-lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
+++++++++++++++++
CMakeLists.txt:
cmake_minimum_required (VERSION 2.8 FATAL_ERROR)
project (Rayleigh2D Fortran)
##################################################
# Add include and link directories to compilation.
# NB: Must happen before add_executable() !
##################################################
# Include modules (.mod files) in Rayleigh2D_Modules folder
include_directories (${CMAKE_CURRENT_BINARY_DIR}/Rayleigh2D_Modules)
# Search for my custom libraries in $HOME (PA).
link_directories ("/Users/paulanto/usr/local/lib/")
include_directories ("/Users/paulanto/usr/local/include/")
link_directories ("/home/gudrun/paulanto/usr/local/lib/")
include_directories ("/home/gudrun/paulanto/usr/local/include/")
add_executable (Rayleigh2D Rayleigh2D.f90)
# The FFT_Modules are treated specially with its own CMakeLists.txt file.
add_subdirectory (FFT_Modules)
##################################################
# Compiler-dependent flags for optimization
##################################################
if (CMAKE_Fortran_COMPILER MATCHES "gfortran")
set (CMAKE_Fortran_FLAGS_RELEASE " -fopenmp -funroll-loops -O3 ")
# This debug flag makes Ingve's surface generation code crash
(27.jan.2011):
# -ffpe-trap=zero,denormal
set (CMAKE_Fortran_FLAGS_DEBUG
" -fopenmp -O0 -g3 -pg -Wall -Wextra -fimplicit-none
-fbounds-check ")
endif (CMAKE_Fortran_COMPILER MATCHES "gfortran")
if (CMAKE_Fortran_COMPILER MATCHES "g95")
set (CMAKE_Fortran_FLAGS_RELEASE " -funroll-loops -O3 ")
set (CMAKE_Fortran_FLAGS_DEBUG
" -O0 -g3 -pg -Wall -Wextra -fimplicit-none -fbounds-check ")
endif (CMAKE_Fortran_COMPILER MATCHES "g95")
if (CMAKE_Fortran_COMPILER MATCHES "xlf")
# Possible optimization flags to include: -qessl -qhot
set (CMAKE_Fortran_FLAGS_RELEASE " -O3 -qsmp=omp ")
set (CMAKE_Fortran_FLAGS_DEBUG " -O1 -qcheck -qdbg ")
endif (CMAKE_Fortran_COMPILER MATCHES "xlf")
if (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
set (CMAKE_Fortran_FLAGS_RELEASE " -O3 -openmp -funroll-loops ")
set (CMAKE_Fortran_FLAGS_DEBUG " -O0 -g -openmp ")
endif (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
##################################################
# Library linking is handled below
##################################################
# Common libraries for all compilers
target_link_libraries (Rayleigh2D Rayleigh2D_Module FFT_Modules fftw3
hdf5 hdf5_hl hdf5_fortran hdf5hl_fortran z)
# Gfortran and G95 calls LAPACK and BLAS by their names
if (CMAKE_Fortran_COMPILER MATCHES "gfortran" OR CMAKE_Fortran_COMPILER
MATCHES "g95")
#target_link_libraries (Rayleigh2D blas lapack)
target_link_libraries (Rayleigh2D goto2)
endif (CMAKE_Fortran_COMPILER MATCHES "gfortran" OR
CMAKE_Fortran_COMPILER MATCHES "g95")
# Xlf calls LAPACK and BLAS by the name "essl"
if (CMAKE_Fortran_COMPILER MATCHES "xlf")
target_link_libraries (Rayleigh2D essl)
endif (CMAKE_Fortran_COMPILER MATCHES "xlf")
# Intel compiler calls LAPACK and BLAS by the name "mkl" (and similar).
if (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
#EXECUTE_PROCESS(COMMAND hostname
#OUTPUT_VARIABLE myhostname
#OUTPUT_STRIP_TRAILING_WHITESPACE)
#if (myhostname STREQUAL "kongull.hpc.ntnu.no")
# On kongull, according to the support people, one should link
# to -lguide. It does not exist on e.g. bakke.
target_link_libraries (Rayleigh2D mkl_intel_lp64 mkl_intel_thread
mkl_core guide)
endif (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
##################################################
# Set up libraries in subdirectories.
# NB: Must happen after compiler flags are set!
##################################################
add_library(Rayleigh2D_Module
Rayleigh2D_Modules/Rayleigh2D_Module.f90
Rayleigh2D_Modules/Rayleigh2D_Utils.f90
Rayleigh2D_Modules/SFL_Error_Handling.f90
Rayleigh2D_Modules/SFL_Fourier.f90
Rayleigh2D_Modules/SFL_ISO_Fortran_Env.f90
Rayleigh2D_Modules/SFL_Logical_Units.f90
Rayleigh2D_Modules/constants.f90
Rayleigh2D_Modules/derived_type_module.f90
Rayleigh2D_Modules/surface_correlated_module.f90
Rayleigh2D_Modules/surface_util_module.f90
Rayleigh2D_Modules/zbcg2_module.f90
Rayleigh2D_Modules/BiCGstab_module.f90
Rayleigh2D_Modules/R_save.f90
Rayleigh2D_Modules/version.f90
)
Arjen Markus
wrote:
Can you also show the error messages when you try to buld the program
via the CMake-
generated makefiles?
Regards,
Arjen
Paul Anton Letnes
Sure. It is loooong. Looks like a linking error to me? The build is from
the "debug" configuration. I ran a build before this one, it appears
that the compilation step is OK, but the linking seems to fail all over
the place.
++++++++++++++
$ make
[ 82%] Built target Rayleigh2D_Module
[ 94%] Built target FFT_Modules
Linking Fortran executable Rayleigh2D
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5close_types_c_':
H5_f.c:(.text+0x34): undefined reference to `H5Tclose'
H5_f.c:(.text+0x78): undefined reference to `H5Tclose'
H5_f.c:(.text+0xa8): undefined reference to `H5Tclose'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5open_c_':
H5_f.c:(.text+0x102): undefined reference to `H5open'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5close_c_':
H5_f.c:(.text+0x122): undefined reference to `H5close'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5get_libversion_c_':
H5_f.c:(.text+0x162): undefined reference to `H5get_libversion'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5check_version_c_':
H5_f.c:(.text+0x1a8): undefined reference to `H5check_version'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5garbage_collect_c_':
H5_f.c:(.text+0x1b2): undefined reference to `H5garbage_collect'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5dont_atexit_c_':
H5_f.c:(.text+0x1d2): undefined reference to `H5dont_atexit'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5init_flags_c_':
H5_f.c:(.text+0x2c0): undefined reference to `H5check_version'
H5_f.c:(.text+0x2db): undefined reference to `H5check_version'
H5_f.c:(.text+0x2f7): undefined reference to `H5check_version'
H5_f.c:(.text+0x313): undefined reference to `H5check_version'
H5_f.c:(.text+0x32f): undefined reference to `H5check_version'
H5_f.c:(.text+0x427): undefined reference to `H5FD_core_init'
H5_f.c:(.text+0x42f): undefined reference to `H5FD_family_init'
H5_f.c:(.text+0x438): undefined reference to `H5FD_log_init'
H5_f.c:(.text+0x441): undefined reference to `H5FD_mpio_init'
H5_f.c:(.text+0x44a): undefined reference to `H5FD_multi_init'
H5_f.c:(.text+0x453): undefined reference to `H5FD_sec2_init'
H5_f.c:(.text+0x45c): undefined reference to `H5FD_stdio_init'
H5_f.c:(.text+0x578): undefined reference to `H5open'
H5_f.c:(.text+0x583): undefined reference to `H5P_CLS_FILE_CREATE_g'
H5_f.c:(.text+0x58b): undefined reference to `H5open'
H5_f.c:(.text+0x591): undefined reference to `H5P_CLS_FILE_ACCESS_g'
H5_f.c:(.text+0x59a): undefined reference to `H5open'
H5_f.c:(.text+0x5a0): undefined reference to `H5P_CLS_DATASET_CREATE_g'
H5_f.c:(.text+0x5a9): undefined reference to `H5open'
H5_f.c:(.text+0x5af): undefined reference to `H5P_CLS_DATASET_XFER_g'
H5_f.c:(.text+0x5b8): undefined reference to `H5open'
H5_f.c:(.text+0x5be): undefined reference to `H5P_CLS_FILE_MOUNT_g'
H5_f.c:(.text+0x5cf): undefined reference to `H5open'
H5_f.c:(.text+0x5d5): undefined reference to `H5P_CLS_ROOT_g'
H5_f.c:(.text+0x5de): undefined reference to `H5open'
H5_f.c:(.text+0x5e4): undefined reference to `H5P_CLS_OBJECT_CREATE_g'
H5_f.c:(.text+0x5ed): undefined reference to `H5open'
H5_f.c:(.text+0x5f3): undefined reference to `H5P_CLS_DATASET_ACCESS_g'
H5_f.c:(.text+0x5fc): undefined reference to `H5open'
H5_f.c:(.text+0x602): undefined reference to `H5P_CLS_GROUP_CREATE_g'
H5_f.c:(.text+0x60b): undefined reference to `H5open'
H5_f.c:(.text+0x611): undefined reference to `H5P_CLS_GROUP_ACCESS_g'
H5_f.c:(.text+0x61a): undefined reference to `H5open'
H5_f.c:(.text+0x620): undefined reference to `H5P_CLS_DATATYPE_CREATE_g'
H5_f.c:(.text+0x629): undefined reference to `H5open'
H5_f.c:(.text+0x62f): undefined reference to `H5P_CLS_DATATYPE_ACCESS_g'
H5_f.c:(.text+0x638): undefined reference to `H5open'
H5_f.c:(.text+0x63e): undefined reference to `H5P_CLS_STRING_CREATE_g'
H5_f.c:(.text+0x647): undefined reference to `H5open'
H5_f.c:(.text+0x64d): undefined reference to `H5P_CLS_ATTRIBUTE_CREATE_g'
H5_f.c:(.text+0x656): undefined reference to `H5open'
H5_f.c:(.text+0x65c): undefined reference to `H5P_CLS_OBJECT_COPY_g'
H5_f.c:(.text+0x665): undefined reference to `H5open'
H5_f.c:(.text+0x66b): undefined reference to `H5P_CLS_LINK_CREATE_g'
H5_f.c:(.text+0x674): undefined reference to `H5open'
H5_f.c:(.text+0x689): undefined reference to `H5P_CLS_LINK_ACCESS_g'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5_f.o):
In function `h5init_types_c_':
H5_f.c:(.text+0x9f1): undefined reference to `H5open'
H5_f.c:(.text+0x9f7): undefined reference to `H5T_NATIVE_INT_g'
H5_f.c:(.text+0x9fc): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xa0c): undefined reference to `H5open'
H5_f.c:(.text+0xa12): undefined reference to `H5T_NATIVE_FLOAT_g'
H5_f.c:(.text+0xa17): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xa27): undefined reference to `H5open'
H5_f.c:(.text+0xa2d): undefined reference to `H5T_NATIVE_DOUBLE_g'
H5_f.c:(.text+0xa32): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xa42): undefined reference to `H5open'
H5_f.c:(.text+0xa48): undefined reference to `H5T_FORTRAN_S1_g'
H5_f.c:(.text+0xa4d): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xa63): undefined reference to `H5Tset_size'
H5_f.c:(.text+0xa77): undefined reference to `H5Tset_strpad'
H5_f.c:(.text+0xa87): undefined reference to `H5open'
H5_f.c:(.text+0xa8d): undefined reference to `H5T_STD_REF_OBJ_g'
H5_f.c:(.text+0xa92): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xaa2): undefined reference to `H5open'
H5_f.c:(.text+0xaa8): undefined reference to `H5T_STD_REF_DSETREG_g'
H5_f.c:(.text+0xaad): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xabd): undefined reference to `H5open'
H5_f.c:(.text+0xac3): undefined reference to `H5T_NATIVE_SCHAR_g'
H5_f.c:(.text+0xac8): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xad8): undefined reference to `H5open'
H5_f.c:(.text+0xade): undefined reference to `H5T_NATIVE_SHORT_g'
H5_f.c:(.text+0xae3): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xaf3): undefined reference to `H5open'
H5_f.c:(.text+0xaf9): undefined reference to `H5T_NATIVE_INT_g'
H5_f.c:(.text+0xafe): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xb0e): undefined reference to `H5open'
H5_f.c:(.text+0xb14): undefined reference to `H5T_NATIVE_LLONG_g'
H5_f.c:(.text+0xb19): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xb29): undefined reference to `H5open'
H5_f.c:(.text+0xb2f): undefined reference to `H5T_NATIVE_FLOAT_g'
H5_f.c:(.text+0xb34): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xb44): undefined reference to `H5open'
H5_f.c:(.text+0xb4a): undefined reference to `H5T_NATIVE_DOUBLE_g'
H5_f.c:(.text+0xb4f): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xb5f): undefined reference to `H5open'
H5_f.c:(.text+0xb65): undefined reference to `H5T_NATIVE_LDOUBLE_g'
H5_f.c:(.text+0xb6a): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xb7a): undefined reference to `H5open'
H5_f.c:(.text+0xb80): undefined reference to `H5T_IEEE_F32BE_g'
H5_f.c:(.text+0xb85): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xb96): undefined reference to `H5open'
H5_f.c:(.text+0xb9c): undefined reference to `H5T_IEEE_F32LE_g'
H5_f.c:(.text+0xba1): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xbb3): undefined reference to `H5open'
H5_f.c:(.text+0xbb9): undefined reference to `H5T_IEEE_F64BE_g'
H5_f.c:(.text+0xbbe): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xbd0): undefined reference to `H5open'
H5_f.c:(.text+0xbd6): undefined reference to `H5T_IEEE_F64LE_g'
H5_f.c:(.text+0xbdb): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xbed): undefined reference to `H5open'
H5_f.c:(.text+0xbf3): undefined reference to `H5T_STD_I8BE_g'
H5_f.c:(.text+0xbf8): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xc09): undefined reference to `H5open'
H5_f.c:(.text+0xc0f): undefined reference to `H5T_STD_I8LE_g'
H5_f.c:(.text+0xc14): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xc25): undefined reference to `H5open'
H5_f.c:(.text+0xc2b): undefined reference to `H5T_STD_I16BE_g'
H5_f.c:(.text+0xc30): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xc41): undefined reference to `H5open'
H5_f.c:(.text+0xc47): undefined reference to `H5T_STD_I16LE_g'
H5_f.c:(.text+0xc4c): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xc5d): undefined reference to `H5open'
H5_f.c:(.text+0xc63): undefined reference to `H5T_STD_I32BE_g'
H5_f.c:(.text+0xc68): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xc79): undefined reference to `H5open'
H5_f.c:(.text+0xc7f): undefined reference to `H5T_STD_I32LE_g'
H5_f.c:(.text+0xc84): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xc95): undefined reference to `H5open'
H5_f.c:(.text+0xc9b): undefined reference to `H5T_STD_I64BE_g'
H5_f.c:(.text+0xca0): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xcb1): undefined reference to `H5open'
H5_f.c:(.text+0xcb7): undefined reference to `H5T_STD_I64LE_g'
H5_f.c:(.text+0xcbc): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xccd): undefined reference to `H5open'
H5_f.c:(.text+0xcd3): undefined reference to `H5T_STD_U8BE_g'
H5_f.c:(.text+0xcd8): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xce9): undefined reference to `H5open'
H5_f.c:(.text+0xcef): undefined reference to `H5T_STD_U8LE_g'
H5_f.c:(.text+0xcf4): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xd05): undefined reference to `H5open'
H5_f.c:(.text+0xd0b): undefined reference to `H5T_STD_U16BE_g'
H5_f.c:(.text+0xd10): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xd21): undefined reference to `H5open'
H5_f.c:(.text+0xd27): undefined reference to `H5T_STD_U16LE_g'
H5_f.c:(.text+0xd2c): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xd3d): undefined reference to `H5open'
H5_f.c:(.text+0xd43): undefined reference to `H5T_STD_U32BE_g'
H5_f.c:(.text+0xd48): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xd59): undefined reference to `H5open'
H5_f.c:(.text+0xd5f): undefined reference to `H5T_STD_U32LE_g'
H5_f.c:(.text+0xd64): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xd71): undefined reference to `H5open'
H5_f.c:(.text+0xd77): undefined reference to `H5T_STD_U64BE_g'
H5_f.c:(.text+0xd7c): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xd89): undefined reference to `H5open'
H5_f.c:(.text+0xd8f): undefined reference to `H5T_STD_U64LE_g'
H5_f.c:(.text+0xd94): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xda1): undefined reference to `H5open'
H5_f.c:(.text+0xda7): undefined reference to `H5T_C_S1_g'
H5_f.c:(.text+0xdac): undefined reference to `H5Tcopy'
H5_f.c:(.text+0xdc3): undefined reference to `H5Tset_size'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dcreate_c_':
H5Df.c:(.text+0x5c): undefined reference to `H5Dcreate2'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dopen_c_':
H5Df.c:(.text+0xc9): undefined reference to `H5Dopen2'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dwritec_c_':
H5Df.c:(.text+0xfd): undefined reference to `H5Dwrite'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dwritec_s_c_':
H5Df.c:(.text+0x12d): undefined reference to `H5Dwrite'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dwritec_1_c_':
H5Df.c:(.text+0x15d): undefined reference to `H5Dwrite'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dwritec_2_c_':
H5Df.c:(.text+0x18d): undefined reference to `H5Dwrite'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dwritec_3_c_':
H5Df.c:(.text+0x1bd): undefined reference to `H5Dwrite'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):H5Df.c:(.text+0x1ed):
more undefined references to `H5Dwrite' follow
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dreadc_c_':
H5Df.c:(.text+0x8dd): undefined reference to `H5Dread'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dreadc_s_c_':
H5Df.c:(.text+0x90d): undefined reference to `H5Dread'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dreadc_1_c_':
H5Df.c:(.text+0x93d): undefined reference to `H5Dread'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dreadc_2_c_':
H5Df.c:(.text+0x96d): undefined reference to `H5Dread'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dreadc_3_c_':
H5Df.c:(.text+0x99d): undefined reference to `H5Dread'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):H5Df.c:(.text+0x9cd):
more undefined references to `H5Dread' follow
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dclose_c_':
H5Df.c:(.text+0x10b4): undefined reference to `H5Dclose'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dget_space_c_':
H5Df.c:(.text+0x10d7): undefined reference to `H5Dget_space'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dget_type_c_':
H5Df.c:(.text+0x10f7): undefined reference to `H5Dget_type'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dget_create_plist_c_':
H5Df.c:(.text+0x1117): undefined reference to `H5Dget_create_plist'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dset_extent_c_':
H5Df.c:(.text+0x114a): undefined reference to `H5Dget_space'
H5Df.c:(.text+0x115e): undefined reference to `H5Sget_simple_extent_ndims'
H5Df.c:(.text+0x1169): undefined reference to `H5Sclose'
H5Df.c:(.text+0x11ec): undefined reference to `H5Dset_extent'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dget_storage_size_c_':
H5Df.c:(.text+0x1237): undefined reference to `H5Dget_storage_size'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dvlen_get_max_len_c_':
H5Df.c:(.text+0x1270): undefined reference to `H5Sget_select_npoints'
H5Df.c:(.text+0x12a1): undefined reference to `H5Dread'
H5Df.c:(.text+0x12d8): undefined reference to `H5Dvlen_reclaim'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dwrite_vl_integer_c_':
H5Df.c:(.text+0x1535): undefined reference to `H5Dwrite'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dread_vl_integer_c_':
H5Df.c:(.text+0x15bb): undefined reference to `H5Sget_select_npoints'
H5Df.c:(.text+0x1611): undefined reference to `H5Dread'
H5Df.c:(.text+0x1678): undefined reference to `H5Dvlen_reclaim'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dwrite_vl_string_c_':
H5Df.c:(.text+0x1792): undefined reference to `H5Dwrite'
H5Df.c:(.text+0x17b0): undefined reference to `H5Dvlen_reclaim'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dread_vl_string_c_':
H5Df.c:(.text+0x1862): undefined reference to `H5Dread'
H5Df.c:(.text+0x1965): undefined reference to `H5Dvlen_reclaim'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dwrite_vl_real_c_':
H5Df.c:(.text+0x1c55): undefined reference to `H5Dwrite'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dread_vl_real_c_':
H5Df.c:(.text+0x1cdb): undefined reference to `H5Sget_select_npoints'
H5Df.c:(.text+0x1d31): undefined reference to `H5Dread'
H5Df.c:(.text+0x1d98): undefined reference to `H5Dvlen_reclaim'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dfillc_c_':
H5Df.c:(.text+0x1dd0): undefined reference to `H5Dfill'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dfill_c_':
H5Df.c:(.text+0x1e00): undefined reference to `H5Dfill'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dfill_integer_c_':
H5Df.c:(.text+0x1e30): undefined reference to `H5Dfill'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dfill_real_c_':
H5Df.c:(.text+0x1e60): undefined reference to `H5Dfill'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dfill_double_c_':
H5Df.c:(.text+0x1e90): undefined reference to `H5Dfill'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dget_space_status_c_':
H5Df.c:(.text+0x1ebf): undefined reference to `H5Dget_space_status'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dcreate_anon_c_':
H5Df.c:(.text+0x1ef1): undefined reference to `H5Dcreate_anon'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Df.o):
In function `h5dget_access_plist_c_':
H5Df.c:(.text+0x1f17): undefined reference to `H5Dget_access_plist'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fcreate_c_':
H5Ff.c:(.text+0x30): undefined reference to `H5Fcreate'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fflush_c_':
H5Ff.c:(.text+0x66): undefined reference to `H5Fflush'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fmount_c_':
H5Ff.c:(.text+0xb1): undefined reference to `H5Fmount'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5funmount_c_':
H5Ff.c:(.text+0x115): undefined reference to `H5Funmount'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fopen_c_':
H5Ff.c:(.text+0x178): undefined reference to `H5Fopen'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5freopen_c_':
H5Ff.c:(.text+0x1b7): undefined reference to `H5Freopen'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fget_create_plist_c_':
H5Ff.c:(.text+0x1d7): undefined reference to `H5Fget_create_plist'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fget_access_plist_c_':
H5Ff.c:(.text+0x1f7): undefined reference to `H5Fget_access_plist'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fis_hdf5_c_':
H5Ff.c:(.text+0x22c): undefined reference to `H5Fis_hdf5'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fclose_c_':
H5Ff.c:(.text+0x264): undefined reference to `H5Fclose'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fget_obj_count_c_':
H5Ff.c:(.text+0x28a): undefined reference to `H5Fget_obj_count'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fget_obj_ids_c_':
H5Ff.c:(.text+0x2ec): undefined reference to `H5Fget_obj_ids'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fget_freespace_c_':
H5Ff.c:(.text+0x427): undefined reference to `H5Fget_freespace'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fget_name_c_':
H5Ff.c:(.text+0x486): undefined reference to `H5Fget_name'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Ff.o):
In function `h5fget_filesize_c_':
H5Ff.c:(.text+0x4df): undefined reference to `H5Fget_filesize'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gcreate_c_':
H5Gf.c:(.text+0x3f): undefined reference to `H5open'
H5Gf.c:(.text+0x45): undefined reference to `H5P_CLS_GROUP_CREATE_g'
H5Gf.c:(.text+0x4a): undefined reference to `H5Pcreate'
H5Gf.c:(.text+0x5e): undefined reference to `H5Pset_local_heap_size_hint'
H5Gf.c:(.text+0x76): undefined reference to `H5Gcreate2'
H5Gf.c:(.text+0x8e): undefined reference to `H5Pclose'
H5Gf.c:(.text+0xcb): undefined reference to `H5Gcreate2'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gopen_c_':
H5Gf.c:(.text+0x119): undefined reference to `H5Gopen2'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gget_obj_info_idx_c_':
H5Gf.c:(.text+0x1aa): undefined reference to `H5Gopen2'
H5Gf.c:(.text+0x1ca): undefined reference to `H5Lget_name_by_idx'
H5Gf.c:(.text+0x1f2): undefined reference to `H5Oget_info_by_idx'
H5Gf.c:(.text+0x225): undefined reference to `H5Gclose'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gn_members_c_':
H5Gf.c:(.text+0x29b): undefined reference to `H5Gget_info_by_name'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gclose_c_':
H5Gf.c:(.text+0x2d4): undefined reference to `H5Gclose'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5glink_c_':
H5Gf.c:(.text+0x34b): undefined reference to `H5Lcreate_hard'
H5Gf.c:(.text+0x369): undefined reference to `H5Lcreate_soft'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5glink2_c_':
H5Gf.c:(.text+0x405): undefined reference to `H5Lcreate_hard'
H5Gf.c:(.text+0x422): undefined reference to `H5Lcreate_soft'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gunlink_c_':
H5Gf.c:(.text+0x48e): undefined reference to `H5Ldelete'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gmove_c_':
H5Gf.c:(.text+0x513): undefined reference to `H5Lmove'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gmove2_c_':
H5Gf.c:(.text+0x5a8): undefined reference to `H5Lmove'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gget_linkval_c_':
H5Gf.c:(.text+0x662): undefined reference to `H5Lget_val'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gset_comment_c_':
H5Gf.c:(.text+0x6ed): undefined reference to `H5Oset_comment_by_name'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gget_comment_c_':
H5Gf.c:(.text+0x78c): undefined reference to `H5Oget_comment_by_name'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gcreate_anon_c_':
H5Gf.c:(.text+0x7dc): undefined reference to `H5Gcreate_anon'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gget_create_plist_c_':
H5Gf.c:(.text+0x807): undefined reference to `H5Gget_create_plist'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gget_info_c_':
H5Gf.c:(.text+0x843): undefined reference to `H5Gget_info'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gget_info_by_idx_c_':
H5Gf.c:(.text+0x8fe): undefined reference to `H5Gget_info_by_idx'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Gf.o):
In function `h5gget_info_by_name_c_':
H5Gf.c:(.text+0x9c6): undefined reference to `H5Gget_info_by_name'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lcopy_c_':
H5Lf.c:(.text+0x66): undefined reference to `H5Lcopy'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lcreate_external_c_':
H5Lf.c:(.text+0x12a): undefined reference to `H5Lcreate_external'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5ldelete_c_':
H5Lf.c:(.text+0x1a0): undefined reference to `H5Ldelete'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lcreate_soft_c_':
H5Lf.c:(.text+0x22c): undefined reference to `H5Lcreate_soft'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lcreate_hard_c_':
H5Lf.c:(.text+0x2d6): undefined reference to `H5Lcreate_hard'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5ldelete_by_idx_c_':
H5Lf.c:(.text+0x35a): undefined reference to `H5Ldelete_by_idx'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lexists_c_':
H5Lf.c:(.text+0x3c7): undefined reference to `H5Lexists'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lget_info_c_':
H5Lf.c:(.text+0x447): undefined reference to `H5Lget_info'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lget_info_by_idx_c_':
H5Lf.c:(.text+0x511): undefined reference to `H5Lget_info_by_idx'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lis_registered_c_':
H5Lf.c:(.text+0x5a4): undefined reference to `H5Lis_registered'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lmove_c_':
H5Lf.c:(.text+0x616): undefined reference to `H5Lmove'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lget_name_by_idx_c_':
H5Lf.c:(.text+0x6df): undefined reference to `H5Lget_name_by_idx'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Lf.o):
In function `h5lget_val_c_':
H5Lf.c:(.text+0x773): undefined reference to `H5Lget_val'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5screate_simple_c_':
H5Sf.c:(.text+0xde): undefined reference to `H5Screate_simple'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sclose_c_':
H5Sf.c:(.text+0x114): undefined reference to `H5Sclose'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5screate_c_':
H5Sf.c:(.text+0x137): undefined reference to `H5Screate'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5scopy_c_':
H5Sf.c:(.text+0x157): undefined reference to `H5Scopy'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_select_hyper_nblocks_c_':
H5Sf.c:(.text+0x177): undefined reference to `H5Sget_select_hyper_nblocks'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_select_elem_npoints_c_':
H5Sf.c:(.text+0x197): undefined reference to `H5Sget_select_elem_npoints'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_select_hyper_blocklist_c_':
H5Sf.c:(.text+0x1cc): undefined reference to `H5Sget_simple_extent_ndims'
H5Sf.c:(.text+0x211): undefined reference to `H5Sget_select_hyper_blocklist'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_select_bounds_c_':
H5Sf.c:(.text+0x400): undefined reference to `H5Sget_simple_extent_ndims'
H5Sf.c:(.text+0x427): undefined reference to `H5Sget_select_bounds'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_select_elem_pointlist_c_':
H5Sf.c:(.text+0x68b): undefined reference to `H5Sget_simple_extent_ndims'
H5Sf.c:(.text+0x6cb): undefined reference to `H5Sget_select_elem_pointlist'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sselect_all_c_':
H5Sf.c:(.text+0x744): undefined reference to `H5Sselect_all'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sselect_none_c_':
H5Sf.c:(.text+0x764): undefined reference to `H5Sselect_none'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sselect_valid_c_':
H5Sf.c:(.text+0x787): undefined reference to `H5Sselect_valid'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_simple_extent_npoints_c_':
H5Sf.c:(.text+0x7a7): undefined reference to `H5Sget_simple_extent_npoints'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_select_npoints_c_':
H5Sf.c:(.text+0x7c7): undefined reference to `H5Sget_select_npoints'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_simple_extent_ndims_c_':
H5Sf.c:(.text+0x7e7): undefined reference to `H5Sget_simple_extent_ndims'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_simple_extent_type_c_':
H5Sf.c:(.text+0x807): undefined reference to `H5Sget_simple_extent_type'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5soffset_simple_c_':
H5Sf.c:(.text+0x835): undefined reference to `H5Sget_simple_extent_ndims'
H5Sf.c:(.text+0x8b3): undefined reference to `H5Soffset_simple'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sset_extent_simple_c_':
H5Sf.c:(.text+0x9c8): undefined reference to `H5Sset_extent_simple'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_simple_extent_dims_c_':
H5Sf.c:(.text+0xa0b): undefined reference to `H5Sget_simple_extent_ndims'
H5Sf.c:(.text+0xa32): undefined reference to `H5Sget_simple_extent_dims'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sis_simple_c_':
H5Sf.c:(.text+0xb97): undefined reference to `H5Sis_simple'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sextent_copy_c_':
H5Sf.c:(.text+0xbb6): undefined reference to `H5Sextent_copy'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sset_extent_none_c_':
H5Sf.c:(.text+0xbd4): undefined reference to `H5Sset_extent_none'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sselect_hyperslab_c_':
H5Sf.c:(.text+0xc17): undefined reference to `H5Sget_simple_extent_ndims'
H5Sf.c:(.text+0xd5f): undefined reference to `H5Sselect_hyperslab'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sget_select_type_c_':
H5Sf.c:(.text+0xda7): undefined reference to `H5Sget_select_type'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sselect_elements_c_':
H5Sf.c:(.text+0xddf): undefined reference to `H5Sget_simple_extent_ndims'
H5Sf.c:(.text+0xf39): undefined reference to `H5Sselect_elements'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sdecode_c_':
H5Sf.c:(.text+0xf85): undefined reference to `H5Sdecode'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sencode_c_':
H5Sf.c:(.text+0xfc5): undefined reference to `H5Sencode'
H5Sf.c:(.text+0x100c): undefined reference to `H5Sencode'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5_fortran.a(H5Sf.o):
In function `h5sextent_equal_c_':
H5Sf.c:(.text+0x1049): undefined reference to `H5Sextent_equal'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltmake_dataset_c_':
H5LTfc.c:(.text+0x148): undefined reference to `H5LTmake_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltmake_dataset_int1_c_':
H5LTfc.c:(.text+0x308): undefined reference to `H5LTmake_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltmake_dataset_int2_c_':
H5LTfc.c:(.text+0x4c8): undefined reference to `H5LTmake_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltmake_dataset_int3_c_':
H5LTfc.c:(.text+0x688): undefined reference to `H5LTmake_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltmake_dataset_fl1_c_':
H5LTfc.c:(.text+0x848): undefined reference to `H5LTmake_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):H5LTfc.c:(.text+0xa08):
more undefined references to `H5LTmake_dataset' follow
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltread_dataset_c_':
H5LTfc.c:(.text+0x2183): undefined reference to `H5LTread_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltread_dataset_int1_c_':
H5LTfc.c:(.text+0x21f3): undefined reference to `H5LTread_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltread_dataset_int2_c_':
H5LTfc.c:(.text+0x2263): undefined reference to `H5LTread_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltread_dataset_int3_c_':
H5LTfc.c:(.text+0x22d3): undefined reference to `H5LTread_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltread_dataset_fl1_c_':
H5LTfc.c:(.text+0x2343): undefined reference to `H5LTread_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):H5LTfc.c:(.text+0x23b3):
more undefined references to `H5LTread_dataset' follow
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltmake_dataset_string_c_':
H5LTfc.c:(.text+0x29ee): undefined reference to `H5LTmake_dataset_string'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltread_dataset_string_c_':
H5LTfc.c:(.text+0x2a5f): undefined reference to `H5LTread_dataset_string'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltset_attribute_int_c_':
H5LTfc.c:(.text+0x2b04): undefined reference to `H5LTset_attribute_int'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltset_attribute_float_c_':
H5LTfc.c:(.text+0x2bb4): undefined reference to `H5LTset_attribute_float'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltset_attribute_double_c_':
H5LTfc.c:(.text+0x2c64): undefined reference to `H5LTset_attribute_double'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltset_attribute_string_c_':
H5LTfc.c:(.text+0x2d2a): undefined reference to `H5LTset_attribute_string'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltget_attribute_int_c_':
H5LTfc.c:(.text+0x2def): undefined reference to `H5LTget_attribute_int'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltget_attribute_float_c_':
H5LTfc.c:(.text+0x2e8f): undefined reference to `H5LTget_attribute_float'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltget_attribute_double_c_':
H5LTfc.c:(.text+0x2f2f): undefined reference to `H5LTget_attribute_double'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltget_attribute_string_c_':
H5LTfc.c:(.text+0x2fcf): undefined reference to `H5LTget_attribute_string'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltget_dataset_ndims_c_':
H5LTfc.c:(.text+0x3041): undefined reference to `H5LTget_dataset_ndims'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltfind_dataset_c_':
H5LTfc.c:(.text+0x30a0): undefined reference to `H5LTfind_dataset'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltget_dataset_info_c_':
H5LTfc.c:(.text+0x3121): undefined reference to `H5LTget_dataset_info'
H5LTfc.c:(.text+0x3151): undefined reference to `H5LTget_dataset_ndims'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltget_attribute_ndims_c_':
H5LTfc.c:(.text+0x3303): undefined reference to `H5LTget_attribute_ndims'
/share/apps/modulessoftware/hdf5/hdf-5.1.8.5-intel/lib/libhdf5hl_fortran.a(H5LTfc.o):
In function `h5ltget_attribute_info_c_':
H5LTfc.c:(.text+0x33c7): undefined reference to `H5LTget_attribute_info'
H5LTfc.c:(.text+0x340c): undefined reference to `H5LTget_attribute_ndims'
make[2]: *** [Rayleigh2D] Error 1
make[1]: *** [CMakeFiles/Rayleigh2D.dir/all] Error 2
make: *** [all] Error 2
Arjen Markus
> In function `h5close_types_c_':
> H5_f.c:(.text+0x34): undefined reference to `H5Tclose'
> H5_f.c:(.text+0x78): undefined reference to `H5Tclose'
> H5_f.c:(.text+0xa8): undefined reference to `H5Tclose'
> In function `h5open_c_':
> H5_f.c:(.text+0x102): undefined reference to `H5open'
> In function `h5close_c_':
> H5_f.c:(.text+0x122): undefined reference to `H5close'
> In function `h5get_libversion_c_':
> H5_f.c:(.text+0x162): undefined reference to `H5get_libversion'
> In function `h5check_version_c_':
> H5_f.c:(.text+0x1a8): undefined reference to `H5check_version'
> In function `h5garbage_collect_c_':
> H5_f.c:(.text+0x1b2): undefined reference to `H5garbage_collect'
> In function `h5dont_atexit_c_':
> H5_f.c:(.text+0x1d2): undefined reference to `H5dont_atexit'
> In function `h5init_flags_c_':
> H5_f.c:(.text+0x2c0): undefined reference to `H5check_version'
> H5_f.c:(.text+0x2db): undefined reference to `H5check_version'
> H5_f.c:(.text+0x2f7): undefined reference to `H5check_version'
> H5_f.c:(.text+0x313): undefined reference to `H5check_version'
> H5_f.c:(.text+0x32f): undefined reference to `H5check_version'
> H5_f.c:(.text+0x427): undefined reference to `H5FD_core_init'
> H5_f.c:(.text+0x42f): undefined reference to `H5FD_family_init'
> H5_f.c:(.text+0x438): undefined reference to `H5FD_log_init'
> H5_f.c:(.text+0x441): undefined reference to `H5FD_mpio_init'
> H5_f.c:(.text+0x44a): undefined reference to `H5FD_multi_init'
> H5_f.c:(.text+0x453): undefined reference to `H5FD_sec2_init'
> H5_f.c:(.text+0x45c): undefined reference to
>
>
> - Tekst uit oorspronkelijk bericht weergeven -...
I think the link statement as run via the CMake option are missing a
few libraries. You should check that the same libraries are used as
for the command-line solution.
At first I suspected a calling convention problem, but that is clearly
not the case. It may also be a matter of the order of the libraries.
In general: if library A requires routines from library B, then
library A should come before library B in the link command.
Regards,
Arjen
Paul Anton Letnes
gfortran but not ifort? Don't they need the same libraries to compile
the same code? (or at any rate, libraries with the same functions in them?)
> At first I suspected a calling convention problem, but that is clearly
> not the case. It may also be a matter of the order of the libraries.
> In general: if library A requires routines from library B, then
> library A should come before library B in the link command.
Is this compiler dependent? Because it does work on gfortran. How can
the ordering be different for different compilers?
Thanks for taking an interest,
Paul.
Arjen Markus
wrote:
>
> This may be worth checking into. However, why is this working for
> gfortran but not ifort? Don't they need the same libraries to compile
> the same code? (or at any rate, libraries with the same functions in them?)
>
It might be something with CMake: I am not sure all HDF5 libraries are
gathered correctly for all compilers.
> > At first I suspected a calling convention problem, but that is clearly
> > not the case. It may also be a matter of the order of the libraries.
> > In general: if library A requires routines from library B, then
> > library A should come before library B in the link command.
>
> Is this compiler dependent? Because it does work on gfortran. How can
> the ordering be different for different compilers?
>
It is or else used to be an issue on Linux: the linker would search a
library only once. It is just a possibility that you can explore if
the other one fails.
Regards,
Arjen
Paul Anton Letnes
I managed to solve the problem by compiling my own version of hdf5 with
mpi disabled, as well as adding the linking and include directories
suggested from h5fc -show. Perhaps there is some problem when using
h5pfc (i.e. parallel hdf5) in a non-mpi program?
Paul
Arjen Markus
>
> - Tekst uit oorspronkelijk bericht weergeven -
Hm, you would at the very least need to include the right MPI
libraries
in the link step, but the missing symbols were related to HDF5, not
MPI.
Odd - maybe you do need a different set of HDF5 libraries in that
case.
Congratulations that you have it working now.
Regards,
Arjen