# Trouble compiling Abinit 10.0.5 with parallel IO

**URL:** <https://discourse.abinit.org/t/trouble-compiling-abinit-10-0-5-with-parallel-io/3748>\
**Category:** Building Abinit\
**Tags:** parallelism, compilation\
**Created:** [July 7, 2025, 4:05pm UTC](https://discourse.abinit.org/t/trouble-compiling-abinit-10-0-5-with-parallel-io/3748 "2025-07-07T16:05:38Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![ethan](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/e/8dc957/32.png) [@ethan](https://discourse.abinit.org/u/ethan)\
**Post date:** [July 7, 2025, 4:05pm UTC](https://discourse.abinit.org/t/trouble-compiling-abinit-10-0-5-with-parallel-io/3748/1 "2025-07-07T16:05:38Z")

</div>

My group uses Abinit on the San Diego supercomputing cluster, and we’ve been doing some longwave calculations that require heavy IO on wavefunction files, so we have been working with one of their staff members to compile Abinit 10.0.5 with parallel IO enabled. We’ve been having some trouble, and I was wondering if you had any input. Essentially, we are able to successfully compile Abinit with the enable-mpi-io flag and have a working Netcdf library (which itself has been compiled with parallelism enabled), but our job fails when we actually try to run a job with iomode=3. Here is a summary of our issue written up by the staffer I’ve been working with, who is able to summarize the issue better than I can:

_I compiled abinit 10.0.5 for a user at SDSC (www.sdsc.edu) on our expanse cluster ( [User Guide](https://www.sdsc.edu/systems/expanse/user_guide.html) ) with --enable-mpi-io set._

_The entire configure line was:_

_./configure --prefix=/expanse/projects/qstore/use300/jpg/abinit-10.0.5-mpio-noopenmp --without-libxml2 --with-optim-flavor=standard WANNIER90\_CPPFLAGS=-I/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/wannier90-3.1.0-4b3fvljf2odknwyqxiznhmnxuf4dgx67/modules WANNIER90\_LIBS=-L/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/wannier90-3.1.0-4b3fvljf2odknwyqxiznhmnxuf4dgx67/lib -lwannier CC=/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/openmpi-4.1.3-oq3qvsvt5mywjzy7xzrfeh6eebiujvbm/bin/mpicc CXX=/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/openmpi-4.1.3-oq3qvsvt5mywjzy7xzrfeh6eebiujvbm/bin/mpic++ FC=/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/openmpi-4.1.3-oq3qvsvt5mywjzy7xzrfeh6eebiujvbm/bin/mpif90 --with-mpi --enable-openmp=no --enable-mpi-io LINALG\_LIBS=-L/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/netlib-scalapack-2.1.0-pywku55redapqs6qxqofuvl67kz5ppks/lib -L/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/openblas-0.3.18-fgk2tlu7bbymzbnkresz4zt5tyfmnbbs/lib -lscalapack -lopenblas --with-linalg-flavor=openblas --with-fft-flavor=fftw3 FFTW3\_CPPFLAGS=-I/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/fftw-3.3.10-qogw3ssyk3cwr5qiwik3eetj22cryewg/include FFTW3\_LIBS=-L/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/fftw-3.3.10-qogw3ssyk3cwr5qiwik3eetj22cryewg/lib -lfftw3 -lfftw3f --with-libxc=/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/libxc-5.1.5-2yb6cx6otiu4gm27djl5yilakk6pc2tb --with-netcdf=/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/netcdf-c-4.8.1-2u4nujbtkkbllgcibtspjzvjahg4em2l --with-netcdf-fortran=/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/netcdf-fortran-4.5.3-i35rncs7ftem7fd2asrefkhbnc572be5_

_with the following environment:_

_gcc/10.2.0_  
_openmpi/4.1.3_  
_wannier90/3.1.0_  
_netlib-scalapack/2.1.0_  
_fftw/3.3.10_  
_netcdf-c/4.8.1_  
_netcdf-fortran/4.5.3_  
_libxc/5.1.5_

_where netcdf-c has parallel-netcdf enabled._

_Running ldd on the executable gives the following for the netcdf libraries (note that parallel netcdf is included):_

_[jpg@login01 abinit-10.0.5]$ ldd src/98\_main/abinit |grep netcdf_

- libnetcdff.so.7 =\> /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/netcdf-fortran-4.5.3-i35rncs7ftem7fd2asrefkhbnc572be5/lib/libnetcdff.so.7 (0x00001555522bb000)\*
- libnetcdf.so.19 =\> /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/netcdf-c-4.8.1-2u4nujbtkkbllgcibtspjzvjahg4em2l/lib/libnetcdf.so.19 (0x0000155551f8c000)\*
- libpnetcdf.so.4 =\> /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/parallel-netcdf-1.12.2-njcetktffwg4tsz5nnrc33muv3p7cdv5/lib/libpnetcdf.so.4 (0x000015554f0fe000)\*

_However when the user ran this executable on her job, she got the following error:_

_— !ERROR_

_src\_file: m\_wfk.F90_

_src\_line: 637_

_mpi\_rank: 0_

_message: |_

_Your netcdf library does not support MPI-IO. Cannot write WFK file with nprocs \> 1_

_Did I do something wrong?_

_Thanks,_

_Jerry Greenberg_  
_SDSC User Services_

Any advice would be much appreciated!

Thanks,

Ethan

---

<div class="post-metadata">

**Author:** ![mverstra](https://discourse.abinit.org/user_avatar/discourse.abinit.org/mverstra/32/92_2.png) [@mverstra](https://discourse.abinit.org/u/mverstra)\
**Post date:** [July 10, 2025, 12:15pm UTC](https://discourse.abinit.org/t/trouble-compiling-abinit-10-0-5-with-parallel-io/3748/2 "2025-07-10T12:15:23Z")

</div>

Hello Ethan,

you need a consistent set of hdf5 netcdf and netcdf-fortran libs with the same parallelization scheme and compilers/mpi versions/everything. In particular for fortran modules the compiler has to be identical to that used to compile abinit itself. I don’t see a module for hdf5, but it’s probably auto-loaded by the netcdf libs. Could you check this, and also provide the content of the (not commented with #) lines in the config.h file?

I _think_ that the pnetcdf library is not actually used at all: it’s a separate project from the netcdf-c compiled with the mpicc compiler.

On my macOS machine, ldd abinit gives the following pertinent lines (installed with homebrew in this case, you should have some equivalent paths in your modules)

```auto
ldd src/98_main/abinit 
/opt/homebrew/opt/netcdf-fortran-parallel/lib/libnetcdff.7.dylib (compatibility version 7.0.0, current version 7.1.0)
/opt/homebrew/opt/netcdf-parallel/lib/libnetcdf.19.dylib (compatibility version 19.0.0, current version 19.0.0)
/opt/homebrew/opt/hdf5-parallel/lib/libhdf5.310.dylib (compatibility version 314.0.0, current version 314.0.0)

```

So from the lib file names you can’t tell whether they are installed with mpi. The abinit configure script make a check on that with h5cc -showconfig, then grepping for parallel flags

Matthieu

---

<div class="post-metadata">

**Author:** ![ethan](https://discourse.abinit.org/letter_avatar_proxy/v4/letter/e/8dc957/32.png) [@ethan](https://discourse.abinit.org/u/ethan)\
**Post date:** [July 10, 2025, 6:03pm UTC](https://discourse.abinit.org/t/trouble-compiling-abinit-10-0-5-with-parallel-io/3748/3 "2025-07-10T18:03:14Z")

</div>

Thanks so much Matthieu! I believe our hdf5 was indeed compiled with MPI consistently with the rest of our build. Here is the result of h5cc -config:

```auto
[jpg@login02 abinit-10.0.5]$ h5cc -showconfig
/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/hdf5-1.10.7-5o4oibcvimawkbouxpkomqvhikvsnnnm/h5cc
dir is /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/hdf5-1.10.7-5o4oibcvimawkbouxpkomqvhikvsnnnm
/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen/gcc-8.5.0/gcc-10.2.0-npcyll4gxjhf4tejksmdzlsl3d3usqpd/bin/gcc -I/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/hdf5-1.10.7-5o4oibcvimawkbouxpkomqvhikvsnnnm/include -L/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/hdf5-1.10.7-5o4oibcvimawkbouxpkomqvhikvsnnnm/lib -lhdf5
[jpg@login02 abinit-10.0.5]$ which h5cc
/cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/hdf5-1.10.7-5o4oibcvimawkbouxpkomqvhikvsnnnm/bin/h5cc

```

This hdf5 was compiled with spack with parallel options turned on:

```auto
[jpg@login02 abinit-10.0.5]$ spack find -v hdf5/5o4oib
==> 1 installed package
-- linux-rocky8-zen2 / gcc@10.2.0 -------------------------------
hdf5@1.10.7+cxx+fortran+hl~ipo+java+mpi+shared+szip~threadsafe+tools api=default build_type=RelWithDebInfo

```

Here is more info for our hdf5 compilation:

```auto

General Information:

HDF5 Version: 1.10.7
Configured on: 2023-04-16
Configured by: Unix Makefiles
Host system: Linux-4.18.0-425.13.1.el8_7.x86_64
Uname information: Linux
Byte sex: little-endian
Installation point: /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/hdf5-1.10.7-5o4oibcvimawkbouxpkomqvhikvsnnnm

Compiling Options:
------------------
Build Mode: RelWithDebInfo
Debugging Symbols: OFF
Asserts: OFF
Profiling: OFF
Optimization Level: OFF

Linking Options:
----------------
Libraries:
Statically Linked Executables: OFF
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: m;dl
Archiver: /usr/bin/ar
Ranlib: /usr/bin/ranlib

Languages:
----------
C: YES
C Compiler: /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/openmpi-4.1.3-oq3qvsvt5mywjzy7xzrfeh6eebiujvbm/bin/mpicc 10.2.0
CPPFLAGS:
H5_CPPFLAGS:
AM_CPPFLAGS:
CFLAGS: -std=c99 -Wno-implicit-function-declaration -fstdarg-opt -fmessage-length=0
H5_CFLAGS: -Wall;-Wcast-qual;-Wconversion;-Wextra;-Wfloat-equal;-Wformat=2;-Winit-self;-Winvalid-pch;-Wmissing-include-dirs;-Wno-c++-compat;-Wno-format-nonliteral;-Wshadow;-Wundef;-Wwrite-strings;-pedantic
AM_CFLAGS:
Shared C Library: YES
Static C Library: YES

Fortran: ON
Fortran Compiler: /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/openmpi-4.1.3-oq3qvsvt5mywjzy7xzrfeh6eebiujvbm/bin/mpif90 10.2.0
Fortran Flags:
H5 Fortran Flags: -Waliasing;-Wall;-Wcharacter-truncation;-Wextra;-Wimplicit-interface;-Wsurprising;-Wunderflow;-pedantic;-ffree-form;-fimplicit-none;-std=f2008;-Warray-temporaries;-Wintrinsics-std;-Wimplicit-procedure;-Wreal-q-constant;-Wfunction-elimination;-Wrealloc-lhs;-Wrealloc-lhs-all;-Wno-c-binding-type;-Wuse-without-only;-Winteger-division;-Wfrontend-loop-interchange
AM Fortran Flags:
Shared Fortran Library: YES
Static Fortran Library: YES

C++: ON
C++ Compiler: /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/openmpi-4.1.3-oq3qvsvt5mywjzy7xzrfeh6eebiujvbm/bin/mpic++ 10.2.0
C++ Flags: -fstdarg-opt -fmessage-length=0
H5 C++ Flags: -Wall;-Wcast-qual;-Wconversion;-Wctor-dtor-privacy;-Weffc++;-Wextra;-Wfloat-equal;-Wformat=2;-Winit-self;-Winvalid-pch;-Wmissing-include-dirs;-Wno-format-nonliteral;-Wnon-virtual-dtor;-Wold-style-cast;-Woverloaded-virtual;-Wreorder;-Wshadow;-Wsign-promo;-Wundef;-Wwrite-strings;-pedantic
AM C++ Flags:
Shared C++ Library: YES
Static C++ Library: YES

JAVA: ON
JAVA Compiler: /cm/shared/apps/spack/0.17.3/cpu/b/opt/spack/linux-rocky8-zen2/gcc-10.2.0/openjdk-11.0.12_7-27cv2psb6xthjbwmjlx53otdbjxch6wg/bin/javac

Features:
---------
Parallel HDF5: ON
Parallel Filtered Dataset Writes: ON
Large Parallel I/O: ON
High-level library: ON
Build HDF5 Tests: OFF
Build HDF5 Tools: ON
Threadsafety: OFF
Default API mapping: v110
With deprecated public symbols: ON
I/O filters (external): DEFLATE DECODE ENCODE
MPE:
Direct VFD:
Mirror VFD:
(Read-Only) S3 VFD:
(Read-Only) HDFS VFD:
dmalloc:
Packages w/ extra debug output:
API Tracing: OFF
Using memory checker: OFF
Memory allocation sanity checks: OFF
Function Stack Tracing: OFF
Use file locking: best-effort
Strict File Format Checks: OFF
Optimization Instrumentation:

```