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I am trying to compile hdf5-1.8.22 using intel oneAPI base toolkit/HPC toolkit 2022.1. The Configuration without intel oneAPI was performed with the following commnad:
CC=$DIR/mpich/bin/mpicc FC=$DIR/mpich/bin/mpif90 CXX=$DIR/mpich/bin/mpicxx CFLAGS=-fPIC ./configure --prefix=$DIR/hdf5 --enable-parallel --enable-fortran --enable-production --enable-shared
The process completed successfully. The configuration with Intel oneAPI looks like this:
CC=$INTEL/oneapi/compiler/latest/linux/bin/intel64/icc CXX=$INTEL/oneapi/compiler/latest/linux/bin/intel64/icpc F77=$INTEL/oneapi/compiler/latest/linux/bin/intel64/ifort MPIF90=$INTEL/oneapi/mpi/latest/bin/mpif90 MPICC=$INTEL/oneapi/mpi/latest/bin/mpicc MPICXX=$INTEL/oneapi/mpi/latest/bin/mpiicpc CFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" CXXFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-I$INTEL/oneapi/mpi/latest/include -L$INTEL/oneapi/mpi/latest/lib" ./configure --prefix=$DIR/hdf5 --enable-parallel --enable-fortran --enable-production --enable-shared --enable-static --enable-hl --with-szlib=$DIR/szip-2.1 --with-zlib=$DIR/zlib-1.2.7
It fails with the following log:
checking for an ANSI C-conforming const... yes checking if the compiler understands __inline__... yes checking if the compiler understands __inline... yes checking if the compiler understands inline... yes checking for __attribute__ extension... yes checking for __func__ extension... yes checking for __FUNCTION__ extension... yes checking for C99 designated initialization support... yes checking how to print long long... %unknownd and %unknownu checking Threads support system scope... no checking enable debugging symbols... no checking enable developer warnings... no checking profiling... no checking optimization level... high checking for debug flags... none checking whether function stack tracking is enabled... no checking whether metadata trace file code is enabled... no checking for API tracing... no checking for instrumented library... no checking whether to clear file buffers... yes checking whether a memory checking tool will be used... no checking for parallel support files... provided by compiler checking whether a simple MPI-IO C program can be linked... no configure: error: unable to link a simple MPI-IO C program
How to fix this error?
UPD: If I use CC=mpiicc the full error log looks like this:
configure:4562: $? = 0 configure:4551: /../../intel/oneapi/mpi/latest/bin/mpiicc -qversion >&5 icc: command line warning #10006: ignoring unknown option '-qversion' ld: cannot find -lmpifort ld: cannot find -lmpi configure:4562: $? = 1 configure:4582: checking whether the C compiler works configure:4604: /../../intel/oneapi/mpi/latest/bin/mpiicc -fPIC -O3 -xHost -ip -fno-alias -align conftest.c >&5 ld: cannot find -lmpifort ld: cannot find -lmpi configure:4608: $? = 1 configure:4646: result: no configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "HDF5" | #define PACKAGE_TARNAME "hdf5" | #define PACKAGE_VERSION "1.8.22" | #define PACKAGE_STRING "HDF5 1.8.22" | #define PACKAGE_BUGREPORT "help@hdfgroup.org" | #define PACKAGE_URL "" | #define PACKAGE "hdf5" | #define VERSION "1.8.22" | /* end confdefs.h. */ | | int | main () | { | | ; | return 0; | } configure:4651: error: in `/../../hdf5-1.8.22': configure:4653: error: C compiler cannot create executables
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Hi,
Thanks for reaching out to us.
We can build the HDF5-1.13.1 application successfully. So we suggest you try any of the latest versions of HDF5.
We followed the below steps to build the application :
git clone https://github.com/HDFGroup/hdf5.git
./autogen.sh
./configure --prefix=/home/intel/hemanth/hdf5 --enable-fortran --enable-shared --enable-parallel --with-pic CC=mpiicc FC=mpiifort CXX=mpiicpc CFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" CXXFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-I/opt/intel/oneapi/mpi/latest/include -L/opt/intel/oneapi/mpi/latest/lib" --with-szlib=/home/intel/hdf5/szip-2.1 --with-zlib=/home/intel/hdf5/zlib-1.2.7
make
Thanks & Regards,
Hemanth.
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Hi,
I come to this link when I was hindered by the similar problem on compiling HDF5-1.12.1 with the Intel oneAPI HPC 2022.1.2.117 on Ubuntu 20.04 system.
Thank you for your suggestion. However, I got other problems...
I tried to git clone the latest HDF5 followed by your code, but the next step in the hdf5 directory, it appeared like
**************************
* HDF5 autogen.sh script *
**************************
dirname: missing operand
Try 'dirname --help' for more information.
Running trace script:
./autogen.sh: 215: bin/trace: Permission denied
(base) huan@grape:~/Downloads/hdf5$
I also tried to add sudo, but it did not work.
(base) huan@grape:~/Downloads/hdf5$
(base) huan@grape:~/Downloads/hdf5$ sudo ./autogen.sh
[sudo] password for huan:
**************************
* HDF5 autogen.sh script *
**************************
dirname: missing operand
Try 'dirname --help' for more information.
dirname: missing operand
Try 'dirname --help' for more information.
Running trace script:
./autogen.sh: 215: bin/trace: Permission denied
(base) huan@grape:~/Downloads/hdf5$
(base) huan@grape:~/Downloads/hdf5$
I also found that there is NO configure file in the hdf5 directory!
Then, I returned to the hdf5 version 1.12.1 and tried your code. Firstly, I did like
(base) huan@grape:~/Downloads/hdf5-1.12.1$ ./autogen.sh
**************************
* HDF5 autogen.sh script *
**************************
dirname: missing operand
Try 'dirname --help' for more information.
Running trace script:
Finished processing HDF5 API calls
Running error generation script:
Generating 'H5Epubgen.h'
Generating 'H5Einit.h'
Generating 'H5Eterm.h'
Generating 'H5Edefin.h'
Running API version generation script:
Generating 'src/H5version.h'
Running overflow macro generation script:
Generating 'H5overflow.h'
/opt/anaconda3/bin/libtoolize --copy --force
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'bin'.
libtoolize: copying file 'bin/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
NOTE: You can ignore the warning about adding -I m4.
We already do this in an included file.
--force -I m4 -I /opt/anaconda3/bin/../share/aclocal
./autogen.sh: 271: --force: not found
(base) huan@grape:~/Downloads/hdf5-1.12.1$
It worked fine, and then I found that "FFLAGS" (behind the FCFLAGS) in your code is NOT in the configure options. Here I show the options below.
Some influential environment variables:
CC C compiler command
CFLAGS C compiler flags
LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
nonstandard directory <lib dir>
LIBS libraries to pass to the linker, e.g. -l<library>
CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
you have headers in a nonstandard directory <include dir>
CPP C preprocessor
FC Fortran compiler command
FCFLAGS Fortran compiler flags
CXX C++ compiler command
CXXFLAGS C++ compiler flags
CXXCPP C++ preprocessor
DOXYGEN_PAPER_SIZE
a4wide (default), a4, letter, legal or executive
LT_SYS_LIBRARY_PATH
User-defined run-time library search path.
Use these variables to override the choices made by `configure' or to help
it to find libraries and programs with nonstandard names/locations.
Should the first "FFLAGS" in your code be "FCFLAGS" ?
And the second "FFLAGS= -I/.../include -L/.../lib " might be "LDFLAGS" ?
So, I tried with
(base) huan@grape:~/Downloads/hdf5-1.12.1$ ./configure --prefix=/opt/hdf5 --enable-fortran --enable-parallel --enable-shared --with-pic CC=mpiicc FC=mpiifort CXX=mpiicpc \
> CFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FCFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" CXXFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" \
> LDFLAGS="-I/opt/intel/oneapi/mpi/latest/include -L/opt/intel/oneapi/mpi/latest/lib" \
> --with-szlib=/opt/szip21 --with-zlib=/opt/zlib121
It seemed fine at first.
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.12.1
Configured on: Thu Mar 3 13:40:17 CST 2022
Configured by: huan@grape
Host system: x86_64-unknown-linux-gnu
Uname information: Linux grape 5.13.0-30-generic #33~20.04.1-Ubuntu SMP Mon Feb 7 14:25:10 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /opt/hdf5
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static, shared
Statically Linked Executables:
LDFLAGS: -I/opt/intel/oneapi/mpi/latest/include -L/opt/intel/oneapi/mpi/latest/lib
H5_LDFLAGS:
AM_LDFLAGS: -L/opt/zlib121/lib -L/opt/szip21/lib
Extra libraries: -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /opt/intel/oneapi/mpi/2021.5.1//bin/mpiicc ( Intel(R) C Intel(R) 64 Compiler Version 2021.5.0 Build 20211109_000000)
CPPFLAGS:
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/opt/zlib121/include -I/opt/szip21/include
C Flags: -fPIC -O3 -xHost -ip -fno-alias -align
H5 C Flags: -std=c99 -Wall -Wcomment -Wdeprecated -Wextra-tokens -Wformat -Wformat-security -Wmain -Wmissing-declarations -Wmissing-prototypes -Wp64 -Wpointer-arith -Wreturn-type -Wshadow -Wstrict-prototypes -Wtrigraphs -Wuninitialized -Wunknown-pragmas -Wunused-function -Wunused-variable -Wwrite-strings -Wextra-tokens -Wformat -Wformat-security -Wic-pointer -Wshadow -Wsign-compare -Wtrigraphs -Wwrite-strings -Wl,-s -O3
AM C Flags:
Shared C Library: yes
Static C Library: yes
Fortran: yes
Fortran Compiler: /opt/intel/oneapi/mpi/2021.5.1//bin/mpiifort ( Intel(R) Fortran Intel(R) 64 Compiler Version 2021.5.0 Build 20211109_000000)
Fortran Flags: -fPIC -O3 -xHost -ip -fno-alias -align
H5 Fortran Flags: -stand:f03 -free -warn:all -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: no
Java: no
Features:
---------
Parallel HDF5: yes
Parallel Filtered Dataset Writes: yes
Large Parallel I/O: yes
High-level library: yes
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Threadsafety: no (recursive RW locks: no)
Default API mapping: v112
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE:
Map (H5M) API: no
Direct VFD: no
Mirror VFD: no
(Read-Only) S3 VFD: no
(Read-Only) HDFS VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
(base) huan@grape:~/Downloads/hdf5-1.12.1$
However, the next step, "make", produced lots of warnings...
H5Tconv.c(8323): warning #2259: non-pointer conversion from "unsigned long long" to "double" may lose significant bits
H5T_CONV_Fx(DOUBLE, ULLONG, double, unsigned long long, 0, ULLONG_MAX);
^
H5Tconv.c(8323): warning #2259: non-pointer conversion from "unsigned long long" to "double" may lose significant bits
H5T_CONV_Fx(DOUBLE, ULLONG, double, unsigned long long, 0, ULLONG_MAX);
^
H5Tconv.c(8323): warning #2259: non-pointer conversion from "unsigned long long" to "double" may lose significant bits
H5T_CONV_Fx(DOUBLE, ULLONG, double, unsigned long long, 0, ULLONG_MAX);
^
H5Tconv.c(8462): warning #2259: non-pointer conversion from "size_t={unsigned long}" to "double" may lose significant bits
double olap_d = HDceil((double)(dst_p->shared->size) /
^
H5Tconv.c(8462): warning #2259: non-pointer conversion from "unsigned long" to "double" may lose significant bits
double olap_d = HDceil((double)(dst_p->shared->size) /
^
H5Tconv.c(8469): warning #2259: non-pointer conversion from "size_t={unsigned long}" to "double" may lose significant bits
double olap_d = HDceil((double)(src_p->shared->size) /
and
./src/H5Ppublic.h(6333): warning #1946: trigraph detected and converted
* <td>????????</td>
^
In file included from ../src/hdf5.h(35),
from h5test.h(27),
from testhdf5.h(22),
from testhdf5.c(36):
../src/H5Ppublic.h(6336): warning #1946: trigraph detected and converted
* <td>PPPP????</td>
^
CC tarray.o
icc: command line remark #10010: option '-fno-alias' is deprecated and will be removed in a future release. See '-help deprecated'
In file included from ../src/hdf5.h(35),
from h5test.h(27),
from testhdf5.h(22),
from tarray.c(22):
../src/H5Ppublic.h(6333): warning #1946: trigraph detected and converted
* <td>????????</td>
^
In file included from ../src/hdf5.h(35),
from h5test.h(27),
from testhdf5.h(22),
from tarray.c(22):
../src/H5Ppublic.h(6336): warning #1946: trigraph detected and converted
* <td>PPPP????</td>
^
CC tattr.o
icc: command line remark #10010: option '-fno-alias' is deprecated and will be removed in a future release. See '-help deprecated'
In file included from ../src/hdf5.h(35),
from h5test.h(27),
from testhdf5.h(22),
from tattr.c(22):
and finally,
-----^
H5TBff_gen.F90(342): warning #7025: This directive is not standard F2003.
!DEC$endif
-----^
libtool: compile: mpiifort -I. -I../../../src -I../../../fortran/src -stand:f03 -free -warn:all -O3 -I../../../fortran/src -I../../../fortran/src -fPIC -O3 -xHost -ip -fno-alias -align -c H5TBff_gen.F90 -fPIC -o H5TBff_gen.o >/dev/null 2>&1
FCLD libhdf5hl_fortran.la
make[3]: Leaving directory '/home/huan/Downloads/hdf5-1.12.1/hl/fortran/src'
Making all in test
make[3]: Entering directory '/home/huan/Downloads/hdf5-1.12.1/hl/fortran/test'
mpiifort -I. -I../../../src -I../../../fortran/src -stand:f03 -free -warn:all -O3 -I../../../fortran/src -I../../../hl/fortran/src -I../../../fortran/test -I../../../fortran/src -I../../../fortran/test -I../../../hl/fortran/src -fPIC -O3 -xHost -ip -fno-alias -align -c -o tstds.o tstds.F90
ifort: command line warning #10158: ignoring option '-warn'; argument must be separate
FCLD tstds
ifort: command line warning #10158: ignoring option '-warn'; argument must be separate
mpiifort -I. -I../../../src -I../../../fortran/src -stand:f03 -free -warn:all -O3 -I../../../fortran/src -I../../../hl/fortran/src -I../../../fortran/test -I../../../fortran/src -I../../../fortran/test -I../../../hl/fortran/src -fPIC -O3 -xHost -ip -fno-alias -align -c -o tstlite.o tstlite.F90
ifort: command line warning #10158: ignoring option '-warn'; argument must be separate
tstlite.F90(1790): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SizeOf_buf_type = STORAGE_SIZE(buf3(1), c_size_t)/STORAGE_SIZE(c_char_'a',c_size_t)
----------------------^
tstlite.F90(1790): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SizeOf_buf_type = STORAGE_SIZE(buf3(1), c_size_t)/STORAGE_SIZE(c_char_'a',c_size_t)
------------------------------------------------------^
tstlite.F90(1801): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SizeOf_buf_type = STORAGE_SIZE(bufr3(1), c_size_t)/STORAGE_SIZE(c_char_'a',c_size_t)
----------------------^
tstlite.F90(1801): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SizeOf_buf_type = STORAGE_SIZE(bufr3(1), c_size_t)/STORAGE_SIZE(c_char_'a',c_size_t)
-------------------------------------------------------^
tstlite.F90(1829): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SizeOf_buf_type = STORAGE_SIZE(buf4(1), c_size_t)/STORAGE_SIZE(c_char_'a',c_size_t)
----------------------^
tstlite.F90(1829): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SizeOf_buf_type = STORAGE_SIZE(buf4(1), c_size_t)/STORAGE_SIZE(c_char_'a',c_size_t)
------------------------------------------------------^
tstlite.F90(1851): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SizeOf_buf_type = STORAGE_SIZE(bufr4(1), c_size_t)/STORAGE_SIZE(c_char_'a',c_size_t)
-------------------------^
tstlite.F90(1851): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SizeOf_buf_type = STORAGE_SIZE(bufr4(1), c_size_t)/STORAGE_SIZE(c_char_'a',c_size_t)
----------------------------------------------------------^
FCLD tstlite
ifort: command line warning #10158: ignoring option '-warn'; argument must be separate
mpiifort -I. -I../../../src -I../../../fortran/src -stand:f03 -free -warn:all -O3 -I../../../fortran/src -I../../../hl/fortran/src -I../../../fortran/test -I../../../fortran/src -I../../../fortran/test -I../../../hl/fortran/src -fPIC -O3 -xHost -ip -fno-alias -align -c -o tstimage.o tstimage.F90
ifort: command line warning #10158: ignoring option '-warn'; argument must be separate
FCLD tstimage
ifort: command line warning #10158: ignoring option '-warn'; argument must be separate
mpiifort -I. -I../../../src -I../../../fortran/src -stand:f03 -free -warn:all -O3 -I../../../fortran/src -I../../../hl/fortran/src -I../../../fortran/test -I../../../fortran/src -I../../../fortran/test -I../../../hl/fortran/src -fPIC -O3 -xHost -ip -fno-alias -align -c -o tsttable.o tsttable.F90
ifort: command line warning #10158: ignoring option '-warn'; argument must be separate
tsttable.F90(561): warning #6379: The structure contains one or more misaligned fields. [PARTICLE_T]
TYPE particle_t
-------^
tsttable.F90(104): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SIZEOF_X = storage_size(bufd(1))/storage_size(c_char_'a')
-------------^
tsttable.F90(104): warning #7416: Fortran 2003 does not allow this intrinsic procedure. [STORAGE_SIZE]
SIZEOF_X = storage_size(bufd(1))/storage_size(c_char_'a')
-----------------------------------^
FCLD tsttable
ifort: command line warning #10158: ignoring option '-warn'; argument must be separate
make[3]: Leaving directory '/home/huan/Downloads/hdf5-1.12.1/hl/fortran/test'
make[3]: Entering directory '/home/huan/Downloads/hdf5-1.12.1/hl/fortran'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/home/huan/Downloads/hdf5-1.12.1/hl/fortran'
make[2]: Leaving directory '/home/huan/Downloads/hdf5-1.12.1/hl/fortran'
make[2]: Entering directory '/home/huan/Downloads/hdf5-1.12.1/hl'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/home/huan/Downloads/hdf5-1.12.1/hl'
make[1]: Leaving directory '/home/huan/Downloads/hdf5-1.12.1/hl'
(base) huan@grape:~/Downloads/hdf5-1.12.1$
Do you have further suggestions? Thanks very much in advance.
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Hi, I am trying to compile hdf5 in my linux computer and followed your advise. The installation is done in the directory
/usr/local
sudo git clone https://github.com/HDFGroup/hd5.git
This creates the directory /usr/local/hdf5
Then, I move to hdf5 and do
sudo ./autogen.sh
The script end fine, with the line
*** SUCCESS ***
But, when I run configure,
sudo ./configure --prefix=/usr/local/hdf5 --enable-fortran --enable-shared --enable-parallel --with-pic CC=mpiicc FC=mpiifort CXX=mpiicpc CFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" CXXFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-I/opt/intel/oneapi/mpi/latest/include -L/opt/intel/oneapi/mpi/latest/lib" --with-szlib=/usr/local/szip --with-zlib=/usr/local/zlib
I get the following:
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking enable warnings as errors... no
checking for config x86_64-pc-linux-gnu... no
checking for config x86_64-pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-pc... no
checking for config linux-gnu... found
checking for config ./config/site-specific/host-cantarer-HP-ENVY-TE01-1xxx... no
checking for clang sanitizer checks... checking build mode... debug
checking for gcc... mpiicc
checking whether the C compiler works... no
configure: error: in `/usr/local/hdf5':
configure: error: C compiler cannot create executables
See `config.log' for more details
But mpiicc is of course working.
Thanks,
Andres
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Hi,
We haven't heard back from you. Could you please provide an update on your issue?
Thanks & Regards,
Hemanth
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Hi,
We assume that your issue is resolved. If you need any additional information, please post a new question as this thread will no longer be monitored by Intel.
Thanks & Regards,
Hemanth.
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Hi,
Trying to compile hdf5-1.14.4-2 using below mentioned command. ( with intel)
CC=icc CXX=icpc FC=ifort MPICC=/home/opt_ohpc_pub/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin/mpiicc MPICXX=/home/opt_ohpc_pub/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin/mpiicpc MPIFC=/home/opt_ohpc_pub/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin/mpiifort CFLAGS='-fPIC -O1 -xHost -ip -fno-alias -align' FFLAGS='-fPIC -O1 -xHost -ip -fno-alias -align' CXXFLAGS='-fPIC -O1 -xHost -ip -fno-alias -align' FFLAGS='-I/home/opt_ohpc_pub/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/include/ -L/home/opt_ohpc_pub/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/lib/' ./configure --prefix=/scratch/um_cdac2/met_models/CDACP_Int/all-dep --enable-fortran --enable-shared --enable-parallel --with-zlib=/scratch/um_cdac2/met_models/CDACP_Int/all-dep
Error is "configure: error: HDF5 requires MPI standard 3.0 or greater"
Output of mpiexec --version
Intel(R) MPI Library for Linux* OS, Version 2019 Update 5 Build 20190806 (id: 7e5a4f84c)
Thanks
Gouri K
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