| Reporter: | |
| Status: | open |
| Milestone: | ET_2020_05 |
| Version: | ET_2020_05 |
| Type: | bug |
| Priority: | blocker |
| Component: | EinsteinToolkit thorn |
Comment (by Lucas Timotheo Sanches):
Hey Roland, sorry for the delay. Looks like the culprit is indeed CPPFLAGS=-D_GNU_SOURCE. Here are my compiler flags from simfactory’s optionlist file:
CFLAGS = -g -std=gnu11 -D_GNU_SOURCE -fcommon CXXFLAGS = -g -std=gnu++11 -fcommon -fpermissive F90FLAGS = -g -fcray-pointer -ffixed-line-length-none
I’m quite sure I’ve got this flag from one of the tutorials in the official site, but now I cant seem to find the exact page that recommends it 
. I’ve managed to use the toolkit successfully with it for some time now but always with the system provided HDF5. I’ve decided to try the bundled version to solve an error that in the end hadn't anything to do with the HD5F lib being used and stumbled upon this.
Also, as you’ve asked, my output of cat /etc/os-release
NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/" CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"
and gcc --version
gcc (GCC) 8.3.0 Copyright (C) 2018 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2492/h5check-fails-to-build