HDF5 Installation Error in the latest Ubuntu 18.04LTS with Intel Compilers
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While I used HDF5 library without any problem with Ubuntu version 16.04 LTS, after I upgraded Ubuntu to Ubuntu 18.04 LTS, I have trouble in installing HDF5 with Intel Fortran and C Compilers.
I successfully installed HDF5 with gcc and gfortran.
But, I need to install HDF5 with Intel Fortran and C Compilers to further usage of scientific computation codes which are only compatible with Intel compilers.
I installed szip-2.1.1 and zlib-1.2.11 in the path of $HOME/LIB using
- ifort version 18.0.2
- icc version 18.0.2 (gcc version 7.0.0 compatibility)
- icpc version 18.0.2 (gcc version 7.0.0 compatibility)
(parallel_studio_xe_2018_update2_cluster_edition, compilers_and_libraries_2018.2.199)
with these flags in bash profile
export CC=icc
export CXX=icpc
export FC=ifort
export F9X=ifort
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FCFLAGS='-O3 -xHost -ip'
and tried to install
hdf5-1.10.2
with following configuration
./configure --prefix=$HOME/LIB --with-zlib=$HOME/LIB --with-szip=$HOME/LIB LD_LIBRARY_PATH=-L/home/scyook/LIB/lib CPPFLAGS=-I/home/scyook/LIB/include --enable-fortran --enable-cxx --enable-fortran2003
However next error message appears.
checking size of size_t... configure: error: in `/home/scyook/LIB/hdf5-1.10.2`:
configure: error: cannot compute sizeof (size_t)
these are the last parts of config.log
. #define SIZEOF_INT32_T 0
. #define SIZEOF_UINT32_T 0
. #define SIZEOF_INT_LEAST32_T 0
. #define SIZEOF_UINT_LEAST32_T 0
. #define SIZEOF_INT_FAST32_T 0
. #define SIZEOF_UINT_FAST32_T 0
. #define SIZEOF_INT64_T 0
. #define SIZEOF_UINT64_T 0
. #define SIZEOF_INT_LEAST64_T 0
. #define SIZEOF_UINT_LEAST64_T 0
. #define SIZEOF_INT_FAST64_T 0
. #define SIZEOF_UINT_FAST64_T 0
configure: exit 77
Could I get help for resolving this issue?
software-installation 18.04 hadoop icc
edited May 13 at 4:36
muru
1
asked May 13 at 4:06
Shimchan Yook
61
add a comment |Â
up vote
1
down vote
favorite
While I used HDF5 library without any problem with Ubuntu version 16.04 LTS, after I upgraded Ubuntu to Ubuntu 18.04 LTS, I have trouble in installing HDF5 with Intel Fortran and C Compilers.
I successfully installed HDF5 with gcc and gfortran.
But, I need to install HDF5 with Intel Fortran and C Compilers to further usage of scientific computation codes which are only compatible with Intel compilers.
I installed szip-2.1.1 and zlib-1.2.11 in the path of $HOME/LIB using
- ifort version 18.0.2
- icc version 18.0.2 (gcc version 7.0.0 compatibility)
- icpc version 18.0.2 (gcc version 7.0.0 compatibility)
(parallel_studio_xe_2018_update2_cluster_edition, compilers_and_libraries_2018.2.199)
with these flags in bash profile
export CC=icc
export CXX=icpc
export FC=ifort
export F9X=ifort
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FCFLAGS='-O3 -xHost -ip'
and tried to install
hdf5-1.10.2
with following configuration
./configure --prefix=$HOME/LIB --with-zlib=$HOME/LIB --with-szip=$HOME/LIB LD_LIBRARY_PATH=-L/home/scyook/LIB/lib CPPFLAGS=-I/home/scyook/LIB/include --enable-fortran --enable-cxx --enable-fortran2003
However next error message appears.
checking size of size_t... configure: error: in `/home/scyook/LIB/hdf5-1.10.2`:
configure: error: cannot compute sizeof (size_t)
these are the last parts of config.log
. #define SIZEOF_INT32_T 0
. #define SIZEOF_UINT32_T 0
. #define SIZEOF_INT_LEAST32_T 0
. #define SIZEOF_UINT_LEAST32_T 0
. #define SIZEOF_INT_FAST32_T 0
. #define SIZEOF_UINT_FAST32_T 0
. #define SIZEOF_INT64_T 0
. #define SIZEOF_UINT64_T 0
. #define SIZEOF_INT_LEAST64_T 0
. #define SIZEOF_UINT_LEAST64_T 0
. #define SIZEOF_INT_FAST64_T 0
. #define SIZEOF_UINT_FAST64_T 0
configure: exit 77
Could I get help for resolving this issue?
software-installation 18.04 hadoop icc
edited May 13 at 4:36
muru
1
asked May 13 at 4:06
Shimchan Yook
61
I guess you could use the available patches cdn-fastly.deb.debian.org/debian/pool/main/h/hdf5/… →debian/patches/*
– Knud Larsen
May 13 at 4:43
add a comment |Â
up vote
1
down vote
favorite
up vote
1
down vote
favorite
While I used HDF5 library without any problem with Ubuntu version 16.04 LTS, after I upgraded Ubuntu to Ubuntu 18.04 LTS, I have trouble in installing HDF5 with Intel Fortran and C Compilers.
I successfully installed HDF5 with gcc and gfortran.
But, I need to install HDF5 with Intel Fortran and C Compilers to further usage of scientific computation codes which are only compatible with Intel compilers.
I installed szip-2.1.1 and zlib-1.2.11 in the path of $HOME/LIB using
- ifort version 18.0.2
- icc version 18.0.2 (gcc version 7.0.0 compatibility)
- icpc version 18.0.2 (gcc version 7.0.0 compatibility)
(parallel_studio_xe_2018_update2_cluster_edition, compilers_and_libraries_2018.2.199)
with these flags in bash profile
export CC=icc
export CXX=icpc
export FC=ifort
export F9X=ifort
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FCFLAGS='-O3 -xHost -ip'
and tried to install
hdf5-1.10.2
with following configuration
./configure --prefix=$HOME/LIB --with-zlib=$HOME/LIB --with-szip=$HOME/LIB LD_LIBRARY_PATH=-L/home/scyook/LIB/lib CPPFLAGS=-I/home/scyook/LIB/include --enable-fortran --enable-cxx --enable-fortran2003
However next error message appears.
checking size of size_t... configure: error: in `/home/scyook/LIB/hdf5-1.10.2`:
configure: error: cannot compute sizeof (size_t)
these are the last parts of config.log
. #define SIZEOF_INT32_T 0
. #define SIZEOF_UINT32_T 0
. #define SIZEOF_INT_LEAST32_T 0
. #define SIZEOF_UINT_LEAST32_T 0
. #define SIZEOF_INT_FAST32_T 0
. #define SIZEOF_UINT_FAST32_T 0
. #define SIZEOF_INT64_T 0
. #define SIZEOF_UINT64_T 0
. #define SIZEOF_INT_LEAST64_T 0
. #define SIZEOF_UINT_LEAST64_T 0
. #define SIZEOF_INT_FAST64_T 0
. #define SIZEOF_UINT_FAST64_T 0
configure: exit 77
Could I get help for resolving this issue?
software-installation 18.04 hadoop icc
edited May 13 at 4:36
muru
1
asked May 13 at 4:06
Shimchan Yook
61
While I used HDF5 library without any problem with Ubuntu version 16.04 LTS, after I upgraded Ubuntu to Ubuntu 18.04 LTS, I have trouble in installing HDF5 with Intel Fortran and C Compilers.
I successfully installed HDF5 with gcc and gfortran.
But, I need to install HDF5 with Intel Fortran and C Compilers to further usage of scientific computation codes which are only compatible with Intel compilers.
I installed szip-2.1.1 and zlib-1.2.11 in the path of $HOME/LIB using
- ifort version 18.0.2
- icc version 18.0.2 (gcc version 7.0.0 compatibility)
- icpc version 18.0.2 (gcc version 7.0.0 compatibility)
(parallel_studio_xe_2018_update2_cluster_edition, compilers_and_libraries_2018.2.199)
with these flags in bash profile
export CC=icc
export CXX=icpc
export FC=ifort
export F9X=ifort
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FCFLAGS='-O3 -xHost -ip'
and tried to install
hdf5-1.10.2
with following configuration
./configure --prefix=$HOME/LIB --with-zlib=$HOME/LIB --with-szip=$HOME/LIB LD_LIBRARY_PATH=-L/home/scyook/LIB/lib CPPFLAGS=-I/home/scyook/LIB/include --enable-fortran --enable-cxx --enable-fortran2003
However next error message appears.
checking size of size_t... configure: error: in `/home/scyook/LIB/hdf5-1.10.2`:
configure: error: cannot compute sizeof (size_t)
these are the last parts of config.log
. #define SIZEOF_INT32_T 0
. #define SIZEOF_UINT32_T 0
. #define SIZEOF_INT_LEAST32_T 0
. #define SIZEOF_UINT_LEAST32_T 0
. #define SIZEOF_INT_FAST32_T 0
. #define SIZEOF_UINT_FAST32_T 0
. #define SIZEOF_INT64_T 0
. #define SIZEOF_UINT64_T 0
. #define SIZEOF_INT_LEAST64_T 0
. #define SIZEOF_UINT_LEAST64_T 0
. #define SIZEOF_INT_FAST64_T 0
. #define SIZEOF_UINT_FAST64_T 0
configure: exit 77
Could I get help for resolving this issue?
software-installation 18.04 hadoop icc
edited May 13 at 4:36
muru
1
asked May 13 at 4:06
Shimchan Yook
61
edited May 13 at 4:36
muru
1
edited May 13 at 4:36
muru
1
edited May 13 at 4:36
muru
1
1
asked May 13 at 4:06
Shimchan Yook
61
asked May 13 at 4:06
Shimchan Yook
61
asked May 13 at 4:06
Shimchan Yook
61
61
I guess you could use the available patches cdn-fastly.deb.debian.org/debian/pool/main/h/hdf5/… →debian/patches/*
– Knud Larsen
May 13 at 4:43
add a comment |Â
I guess you could use the available patches cdn-fastly.deb.debian.org/debian/pool/main/h/hdf5/… →debian/patches/*
– Knud Larsen
May 13 at 4:43
I guess you could use the available patches cdn-fastly.deb.debian.org/debian/pool/main/h/hdf5/… →
debian/patches/*– Knud Larsen
May 13 at 4:43
I guess you could use the available patches cdn-fastly.deb.debian.org/debian/pool/main/h/hdf5/… →
debian/patches/*– Knud Larsen
May 13 at 4:43
add a comment |Â
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I guess you could use the available patches cdn-fastly.deb.debian.org/debian/pool/main/h/hdf5/… →
debian/patches/*– Knud Larsen
May 13 at 4:43