Can't find H5FD_npio_init in libhdf5_fortran.so.8

[xkong]

Hi There,

I was trying to output the results in hdf5 format. However, I have got the following messages:

pflotran: symbol lookup error: /pflotran/petsc/arch-linux2-c-debug/lib/libhdf5_fortran.so.8: undefined symbol: H5FD_mpio_init

I have used nm -D to confirm that there is no H5FD_mpio_init in libhdf5_fortran.so.8.

I appreciate if someone could help me resolve this problem. Thanks.

[Hammond, Glenn E]

Your HDF5 does not have the correct functions for parallel I/O. Was HDF5 compiled by PETSc configure?

Glenn

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[xkong]

Hi Glenn,

Thanks for your suggestion. Yes, the current HDF5 was complied with PETSc configure. I have copied the following information from the configure.log. Let me know if there are anything inconsistent. Do we need to install scorpio for using hdf5?

Best, Kong


SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.12
Configured on: Mon May 30 17:07:02 CEST 2016
Configured by: ...@...
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux euler02 2.6.32-504.1.3.el6.euler.x86_64 #1 SMP Tue Nov 18 14:25:50 CET 2014 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries: static, shared
Installation point: /pflotran/petsc/arch-linux2-c-debug
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /pflotran/petsc/arch-linux2-c-debug/bin/mpicc
CFLAGS: -fPIC -g3 -O0
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -ldl -lm
Archiver: /usr/bin/ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: /pflotran/petsc/arch-linux2-c-debug/bin/mpif90
Fortran 2003 Compiler: no
Fortran Flags: -fPIC -ffree-line-length-0 -g -O0
H5 Fortran Flags:
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: no
Features:
---------
Parallel HDF5: yes
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE:
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
==================================================================
Running make install on HDF5; this may take several minutes
==================================================================

[benjami...@gmail.com]

Kong,

I had a similar issue with my HDF5 installation and found the cause of the problem to be a native installation of HDF5 on the supercomputer operating system- In spite of the fact that I had installed HDF5 alongside PETSC, the native HDF5 was overriding the PETSC installation.  I solved this problem by adding the following lines to my ~./bashrc file:

export LD_LIBRARY_PATH=/path/to/my/hdf5/installation:$LD_LIBRARY_PATH

Where '/path/to/my/hdf5/installation' is the directory within the PETSC installation directory where the file libhdf5.so files is found.

Ben

[xkong]

Hi Ben,

Thanks. I first added the library path to LD_LIBRARY_PATH as you suggested, then recompiled the program. It works perfectly now.

Cheers, Kong