“make check” fails when compiling parallel HDF5 with intel compilers!

Farrokh_A_ — Sat, 22 Apr 2017 05:06:06 GMT

Greetings,

I have problem in "make check" of compiling parallel HDF5 using Intel Compilers on CentOS 6.5 64bit. I exactly follow the procedure described in this page but still get this error:

Testing  t_pflush1
============================
 t_pflush1  Test Log
============================
Testing H5Fflush (part1)                                              *** Hint ***
You can use environment variable HDF5_PARAPREFIX to run parallel test files in a
different directory or to add file type prefix. E.g.,
   HDF5_PARAPREFIX=pfs:/PFS/user/me
   export HDF5_PARAPREFIX
*** End of Hint ***
rank 5 in job 8  iwf3_56776   caused collective abort of all ranks
  exit status of rank 5: return code 0
rank 4 in job 8  iwf3_56776   caused collective abort of all ranks
  exit status of rank 4: return code 0
0.04user 0.01system 0:00.31elapsed 19%CPU (0avgtext+0avgdata 47024maxresident)k
0inputs+0outputs (0major+7458minor)pagefaults 0swaps
make[4]: *** [t_pflush1.chkexe_] Error 1
make[4]: Leaving directory `/home/iwf/hdf5/hdf5-1.8.18/testpar'
make[3]: *** [build-check-p] Error 1
make[3]: Leaving directory `/home/iwf/hdf5/hdf5-1.8.18/testpar'
make[2]: *** [test] Error 2
make[2]: Leaving directory `/home/iwf/hdf5/hdf5-1.8.18/testpar'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/iwf/hdf5/hdf5-1.8.18/testpar'
make: *** [check-recursive] Error 1

any idea?

My configuration summary:

SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
           HDF5 Version: 1.8.18
          Configured on: Wed Apr 19 14:41:23 +0430 2017
          Configured by: iwf@iwf3
         Configure mode: production
            Host system: x86_64-unknown-linux-gnu
          Uname information: Linux iwf3 2.6.32-504.23.4.el6.x86_64 #1 SMP Tue Jun 9 20:57:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
               Byte sex: little-endian
              Libraries: static, shared
         Installation point: /home/iwf/hdf5/1.8.18

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /opt/intel//impi/5.0.1.035/intel64/bin/mpicc ( built with gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC))
                         CFLAGS: 
                      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 -Wno-long-long -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 -Wnonnull -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 -O3
                      AM_CFLAGS: 
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/home/iwf/zlib/1.2.11//include
               Shared C Library: yes
               Static C Library: yes
  Statically Linked Executables: no
                        LDFLAGS: 
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/home/iwf/zlib/1.2.11//lib
        Extra libraries: -lz -ldl -lm 
               Archiver: ar
             Ranlib: ranlib
          Debugged Packages:
 API Tracing: no

Languages:
----------
                        Fortran: no

                            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)
                            MPE: 
                     Direct VFD: no
                        dmalloc: no
Clear file buffers before write: yes
           Using memory checker: no
         Function Stack Tracing: no
      Strict File Format Checks: no
   Optimization Instrumentation: no

Hi,

Dmitry_S_Intel — Thu, 27 Apr 2017 08:03:53 GMT

Hi,

Please try with Intel(R) Compiler, the log shows that you are using GCC for MPI version.

To use Intel(R) Compiler you need to use mpiicc instead of mpicc.

Also Intel(R) MPI Library version 5.0.1 is quite old, please consider upgrade to version 2017 Update 2 https://software.intel.com/en-us/intel-mpi-library/

Dmitry

topic Hi, in Intel® MPI Library

“make check” fails when compiling parallel HDF5 with intel compilers!

Hi,