topic How to build HDF5 using Intel compiler? in Intel® MPI Library

How to build HDF5 using Intel compiler?

TamnaSidharth — Thu, 03 Feb 2022 09:40:38 GMT

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

Re: How to build HDF5 using Intel compiler?

HemanthCH_Intel — Mon, 07 Feb 2022 05:27:00 GMT

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.

Re:How to build HDF5 using Intel compiler?

HemanthCH_Intel — Fri, 11 Feb 2022 10:33:57 GMT

Hi,

We haven't heard back from you. Could you please provide an update on your issue?

Thanks & Regards,

Hemanth

Re:How to build HDF5 using Intel compiler?

HemanthCH_Intel — Fri, 18 Feb 2022 09:33:00 GMT

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.

Re: How to build HDF5 using Intel compiler?

HuanWang — Thu, 03 Mar 2022 08:48:23 GMT

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.

Re: How to build HDF5 using Intel compiler?

Andres89 — Wed, 04 Oct 2023 16:21:23 GMT

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

Re: How to build HDF5 using Intel compiler?

GouriKadam — Mon, 22 Jul 2024 10:54:04 GMT

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