Problem with NetCDF installation and SZIP

manuelbogoni commented 4 years ago

Environment Information

Feel free to skip this if the issue is related to documentation, a feature request, or general discussion.

What platform are you using? (please provide specific distribution/version in summary)
- [x] Linux CentOs 17.4
32 and/or 64 bit?
- [x] 64-bit
What build system are you using?
- [x] autotools (configure)

Summary and steps to reproduce the issue

I am trying to compile NetCDF-c-4.7.4.

Environmental variables are set as follows:

CXX=mpiicpc
F90=mpiifort
F77=mpiifort
FC=mpiifort
CC=mpiicc
CPP="mpiicc -EP"

Prior to NetCDF, I installed the following packages, with the previous environmental variables:

ZLIB 1.2.11 (just --prefix)
SZIP 2.1.1 (just --prefix)
HDF5 1.12.0 (--prefix --with-szip --with-zlib --enable-fortran --enable-fortran2003 --enable-hl --enable-gpfs --enable-parallel --enable-build-mode=production --enable-optimization=high)
PNetCDF 1.12.1 (-- prefix, --enable-netcdf4)

New environmental variables related to NetCDF are:

CPPFLAGS="-I${path to HDF5}/include -I${path to PNetCDF}/include"
LDFLAGS="-L${path to HDF5}/lib -L${path to PNetCDF}/lib"

NetCDF configuration is set as --enable-pnetcdf --enable-parallel-tests --prefix --enable-remote-fortran-bootstrap.

My issue

The issue rises along with make check .

make[3]: Entering directory `/galileo/home/userexternal/mbogoni0/LIBRARIES/NETCDF/netcdf-c-4.7.4/source/nc_test4'
PASS: tst_dims
PASS: tst_dims2
PASS: tst_dims3
[ ...some other passed tests... ]
PASS: tst_v2
PASS: run_grp_rename.sh
PASS: tst_misc.sh
PASS: tst_szip.sh
PASS: tst_filter.sh
PASS: test_filter_reg

FAIL: run_par_test.sh
============================================================================
Testsuite summary for netCDF 4.7.4
============================================================================
# TOTAL: 77
# PASS:  76
# SKIP:  0
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0
============================================================================
See nc_test4/test-suite.log
Please report to support-netcdf@unidata.ucar.edu
============================================================================
make[3]: *** [test-suite.log] Error 1

From nc_test4/test-suite.log:

_*** testing szip compression with parallel I/O...Sorry! Unexpected result, tst_parallel5.c, line: 344
 ./run_par_test.sh: line 36: 27324 Killed                  mpiexec -n 4 ./tst_parallel5
FAIL run_par_test.sh (exit status: 137)_

edwardhartnett commented 4 years ago

Thanks for reporting this!

Can you post your libnetcdf.settings file?

manuelbogoni commented 4 years ago

Thanks for reporting this!

Can you post your libnetcdf.settings file?

# NetCDF C Configuration Summary
==============================

# General
-------
NetCDF Version:     4.7.4
Dispatch Version:       2
Configured On:      Tue Aug 25 16:22:41 CEST 2020
Host System:        x86_64-pc-linux-gnu
Build Directory:    /home/LIBRARIES/NETCDF/netcdf-c-4.7.4/source
Install Prefix:         /home/LIBRARIES/NETCDF/netcdf-c-4.7.4

# Compiling Options
-----------------
C Compiler:     /compilers/intel/pe-xe-2018/binary/impi/2018.4.274/bin64/mpiicc
CFLAGS:         -O3 -xHost -ip
CPPFLAGS:       -I/home/LIBRARIES/HDF5/hdf5-1.12.0/include -I/home/LIBRARIES/PNETCDF/pnetcdf-1.12.1/include
LDFLAGS:        -L/home/LIBRARIES/HDF5/hdf5-1.12.0/lib -L/home/LIBRARIES/PNETCDF/pnetcdf-1.12.1/lib
AM_CFLAGS:      
AM_CPPFLAGS:        
AM_LDFLAGS:     
Shared Library:     yes
Static Library:     yes
Extra libraries:    -lpnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl 

# Features
--------
NetCDF-2 API:       yes
HDF4 Support:       no
HDF5 Support:       yes
NetCDF-4 API:       yes
NC-4 Parallel Support:  yes
PnetCDF Support:    yes
DAP2 Support:       yes
DAP4 Support:       yes
Byte-Range Support: no
Diskless Support:   yes
MMap Support:       no
JNA Support:        no
CDF5 Support:       yes
ERANGE Fill Support:    yes
Relaxed Boundary Check: yes
SZIP Support:           yes
SZIP Write Support:     yes
Parallel Filters:       yes

edwardhartnett commented 2 years ago

OK, can you try this with the recent 4.8.1 release?

We have just concluded a study of compression methods, and szip worked out of the box for us on all platforms...

edwardhartnett commented 2 years ago

If this cannot be reproduced, this issue should be closed.

szip is well-tested in current main branch.

edwardhartnett commented 2 years ago

I believe this issue can be closed.

Unidata / netcdf-c