Stuck trying to build hdf5 from source

I am trying to build hdf5 1.10.7 from source. I have been following these instructions. The only change I made was to add CC=/usr/local/bin/mpicc in front of the ./configure command.

For some reason, when I enter the ./configure command, my machine gets stuck on checking build system type.... It’s been this way for about 40 minutes… I have heard that building hdf5 may take a while, but is something possibly wrong?

Any help is appreciated as I’ve been troubleshooting for hours to no avail.

40 mins is unusual. BTW: my preference is openmpi, and I didn’t see any pointers in the tutorial regarding parallel filesystem, from the source distribution root directory please read: less release_docs/INSTALL_parallel Here is the relevant excerpt for you:

1.1. Requirements
-----------------
PHDF5 requires an MPI compiler with MPI-IO support and a POSIX compliant
(Ref. 1) parallel file system.

That document is incorrect. You don’t need a parallel file system for parallel HDF5. We have exactly zero parallel file systems installed on THG machines and we build and test parallel HDF5 every day.

So any idea why I’m getting this error? I’m on Ubuntu 16.04.

Also, when I try to build any version below 1.10.7, I get the following error:

/home/username/hdf5-1.10.6/bin/missing: line 3: $'\r': command not found /home/username/hdf5-1.10.6/bin/missing: line 5: $'\r': command not found /home/username/hdf5-1.10.6/bin/missing: line 8: $'\r': command not found /home/username/hdf5-1.10.6/bin/missing: line 13: $'\r': command not found /home/username/hdf5-1.10.6/bin/missing: line 18: $'\r': command not found /home/username/hdf5-1.10.6/bin/missing: line 21: $'\r': command not found /home/username/hdf5-1.10.6/bin/missing: line 26: $'\r': command not found /home/username/hdf5-1.10.6/bin/missing: line 32: syntax error near unexpected token$‘in\r’’
'home/username/hdf5-1.10.6/bin/missing: line 32: case $1 in configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk 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 configure: error: cannot run /bin/bash bin/config.sub

EDIT: i tried building the tar.bz file instead of the .zip file for 1.10.6 and I’m back to getting stuck on checking build system type.....

It looks like the autotools-generated files somehow got out of date. It’ll probably help if you tell us exactly what you are doing at each step, starting with unzipping the tarball.

Hi, sorry for the delay. Here is what I’m doing:

Download hdf5-1.10.7.zip from here.
Using Ubuntu GUI, extract into Home folder.
In cmd:

cd hdf5-10.0.7
export CC=mpicc
./configure --enable-parallel --prefix=/usr/local/hdf5 --enable-shared

All commands when I try without Ubuntu GUI:

cd /tmp/mozilla_username0
tar -xf hdf5-1.10.7.tar.gz -C /home/username
cd /home/username/hdf5-1.10.7; export CC=mpicc
./configure --enable-parallel --enable-shared --prefix=/usr/local/hdf5

For both, I get the following output:

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
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... 

Can you build serial HDF5? If you just build with ./configure --prefix=/usr/local/hdf5 --enable-shared, does that work?

I am able to build serial hdf5. However (this might be a separate issue - in which case not current priority), I am getting lots of overflow warnings when I do make, make check, and make install. For example:

hdfgifwr.c:319:1: warning: assuming signed overflow does not occur when changing X +- C1 cmp C2 to X cmp C2 -+ C1 [-Wstrict-overflow]

Not sure if relevant to building parallel, though. Anyway, if the issue seems to be installing pHDF5 - any recommended solutions? I need to use parallel HDF5.

Thanks