Install errors - hd5-1.10.4


Hi, just joined to get help with installing.

I"m on Amazon Linux.
I installed gcc.

I need HDF5 for a NETCDF program, and used their recommendation on configuration, which is:
./configure --prefix=/usr/local/hdf5 --with-zlib=/lib64 --enable-hl

There are a number of errors in the config.log. Here are some at the top.

gcc: error: unrecognized command line option ‘-V’
gcc: error: unrecognized command line option ‘-qversion’; did you mean ‘–version’?
conftest.c:11:10: fatal error: ac_nonexistent.h: No such file or directory
conftest.c:57:20: error: expected expression before ‘)’ token
if (sizeof ((off_t)))
I’d like to include the entire config.log file, but it says new users can’t upload files.

Any help is appreciated.



First, please make sure that gcc works with some simple C program.

Errors in config.log file may be OK. What is the output from the ./configure command? Could you capture it in a file

./configure --prefix=/usr/local/hdf5 --with-zlib=/lib64 --enable-hl >&c.log&

and check if it finishes with printing SUMMARY of HDF5 configuration?

If configure fails, then you will need to find in the config.log file the last test that fails to get a better clue.

I will check with our FORUM gurus why you couldn’t submit a file.

Thank you!



Hi Elena,

I confirmed that gcc does indeed work.

Since, I can’t attach files (as a new member), here is the output from the configure:

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe 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... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'gcc' is GNU gcc-7.3.1
expr: syntax error
checking for config ./config/site-specific/host-ip-172-31-33-210.ec2.internal... no
checking for config ./config/site-specific/host-ec2.internal... no
checking for config ./config/site-specific/host-internal... no
checking build mode... production
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking if unsupported combinations of configure options are allowed... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking whether byte ordering is bigendian... no
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of unsigned... 4
checking size of long... 8
checking size of long long... 8
checking size of __int64... 0
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of __float128... 16
checking size of _Quad... 0
checking quadmath.h usability... yes
checking quadmath.h presence... yes
checking for quadmath.h... yes
checking maximum decimal precision for C... 33
checking if Fortran interface enabled... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking dependency style of g++... none
checking how to run the C++ preprocessor... /lib/cpp
configure: error: in `/home/ec2-user/captain/setup_files/hdf5-1.10.4':
configure: error: C++ preprocessor "/lib/cpp" fails sanity check
See `config.log' for more details


It looks like this is the last of the errors:

|                    Syntax error
configure:8984: /lib/cpp   conftest.cpp
cpp: error trying to exec 'cc1plus': execvp: No such file or directory
configure:8984: $? = 1
configure: failed program was:
| /* confdefs.h */


It looks like I can now upload the config.log file:

config.log (67.9 KB)


Please try to set up CXXCPP=‘g++ -E’ and reconfigure.



Elena, I’m not exactly sure if I understand what you are asking me to try.
Are you saying to set an environmental variable, CXXCPP?



Yes, please set environment variable CXXCPP to “g++ -E” (it looks like g++ is installed on your system)


Success on the configure! I had to install gcc-c++. I set the CXXCPP bash environmental variable, and it configured.

It looks like a got an error on “make check”. Here’s the end of the output:

h5repack tests failed with 1 errors.
2.77user 0.76system 0:02.71elapsed 130%CPU (0avgtext+0avgdata 13344maxresident)k
8872inputs+21728outputs (1major+706070minor)pagefaults 0swaps
make[6]: *** [] Error 1
make[6]: Leaving directory `/mnt/captain/setup_files/hdf5-1.10.4/tools/test/h5repack'
make[5]: *** [build-check-s] Error 2
make[5]: Leaving directory `/mnt/captain/setup_files/hdf5-1.10.4/tools/test/h5repack'
make[4]: *** [test] Error 2
make[4]: Leaving directory `/mnt/captain/setup_files/hdf5-1.10.4/tools/test/h5repack'
make[3]: *** [check-am] Error 2
make[3]: Leaving directory `/mnt/captain/setup_files/hdf5-1.10.4/tools/test/h5repack'
make[2]: *** [check-recursive] Error 1
make[2]: Leaving directory `/mnt/captain/setup_files/hdf5-1.10.4/tools/test'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/mnt/captain/setup_files/hdf5-1.10.4/tools'
make: *** [check-recursive] Error 1

do i need to address this error, before doing a make install



There should be error or failure messages earlier in the output that may shed more light on the problem. Can you upload the log from “make check”, or else search for “FAILED”, “Error” or “error” and post what you find there?


Here is the line that failed:
Verifying h5diff output h5repack_objs.h5 out-gt_mallocsize.h5repack_obFAILED

I’ve attached the make check output here:
make.log (51.6 KB)


Any idea on that error? Thanks.


We think you may be able to work around the issue by removing ‘-c’ after diff in these 6 lines in 2 files in test/h5repack:

216: test yes = “$verbose” && diff -c $expect1 $actual1 |sed ‘s/^/ /’

232: test yes = “$verbose” && diff -c $expect2 $actual2 |sed ‘s/^/ /’

44: DIFF=‘diff -c’

692: test yes = “$verbose” && diff -c $expect $actual |sed ‘s/^/ /’

800: test yes = “$verbose” && diff -c $expect $actual |sed ‘s/^/ /’

852: test yes = “$verbose” && diff -c $expect $actual |sed ‘s/^/ /’

These are the source files. You can make the changes in the same lines in and (in the build directory) after you’ve configured. If you do it in the .in files, you’ll need to run configure again to get the changes into the scripts run be make check. Conversely, if you make the changes in the .sh files and not in the files, configuring again will recreate the .sh files without the changes.


Thanks. I edited the .sh files and removed the -c diff option, then ran make check again, but still got the same error with the h5diff:

Verifying h5diff output h5repack_objs.h5 out-gt_mallocsize.h5repack_obFAILED


Any other suggestions to help me with this error? Thank you.


Hey all

I am installing hdf5-1.8.15-patch1 on my Ubuntu 16.04 LTS OS.
I am following the below procedures:

tar -xf hdf5-1.8.15-patch1.tar
cd hdf5-1.8.15-patch1
mkdir build && cd build
…/configure --prefix=/home/diehl/local/hdf5-1.8.15/ --enable-parallel
make -j
make test
make install
cd …/…

At the time of make test I am getting 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.,
*** End of Hint ***

mpiexec has exited due to process rank 0 with PID 0 on
node anirban-desktop exiting improperly. There are three reasons this could occur:

  1. this process did not call “init” before exiting, but others in
    the job did. This can cause a job to hang indefinitely while it waits
    for all processes to call “init”. By rule, if one process calls “init”,
    then ALL processes must call “init” prior to termination.

  2. this process called “init”, but exited without calling “finalize”.
    By rule, all processes that call “init” MUST call “finalize” prior to
    exiting or it will be considered an “abnormal termination”

  3. this process called “MPI_Abort” or “orte_abort” and the mca parameter
    orte_create_session_dirs is set to false. In this case, the run-time cannot
    detect that the abort call was an abnormal termination. Hence, the only
    error message you will receive is this one.

This may have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).

You can avoid this message by specifying -quiet on the mpiexec command line.

Command exited with non-zero status 1
0.09user 0.08system 0:01.07elapsed 16%CPU (0avgtext+0avgdata 16872maxresident)k
0inputs+22256outputs (40major+22958minor)pagefaults 0swaps
Makefile:1296: recipe for target ‘t_pflush1.chkexe_’ failed
make[4]: *** [t_pflush1.chkexe_] Error 1
make[4]: Leaving directory ‘/home/anirban/local/hdf5-1.8.15/build/testpar’
Makefile:1371: recipe for target ‘build-check-p’ failed
make[3]: *** [build-check-p] Error 1
make[3]: Leaving directory ‘/home/anirban/local/hdf5-1.8.15/build/testpar’
Makefile:1276: recipe for target ‘test’ failed
make[2]: *** [test] Error 2
make[2]: Leaving directory ‘/home/anirban/local/hdf5-1.8.15/build/testpar’
Makefile:1079: recipe for target ‘check-am’ failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory ‘/home/anirban/local/hdf5-1.8.15/build/testpar’
Makefile:576: recipe for target ‘check-recursive’ failed
make: *** [check-recursive] Error 1

Help me with some solution.