Stuck trying to build hdf5 from source


#1

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.


#2

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.

#3

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.


#4

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.....


#5

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.


#6

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... 

#7

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


#8

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