From b3acbb8af66a9dbf7b436e942cfa648d3ed5c65e Mon Sep 17 00:00:00 2001
From: chen-jan <chen_aka_jan@163.com>
Date: Mon, 7 Aug 2023 11:19:23 +0800
Subject: [PATCH] fix build error && test error

---
 gromacs-gcc11.patch | 24 ++++++++++++++++++++++++
 gromacs.spec        | 10 +++++++++-
 2 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 gromacs-gcc11.patch

diff --git a/gromacs-gcc11.patch b/gromacs-gcc11.patch
new file mode 100644
index 0000000..a5153dd
--- /dev/null
+++ b/gromacs-gcc11.patch
@@ -0,0 +1,24 @@
+diff --git a/src/gromacs/awh/biasparams.cpp b/src/gromacs/awh/biasparams.cpp
+index f4db497..87e0a40 100644
+--- a/src/gromacs/awh/biasparams.cpp
++++ b/src/gromacs/awh/biasparams.cpp
+@@ -47,6 +47,7 @@
+ #include "biasparams.h"
+ 
+ #include <cmath>
++#include <limits>
+ 
+ #include <algorithm>
+ 
+diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp
+index 8550271..d259b66 100644
+--- a/src/gromacs/mdrun/minimize.cpp
++++ b/src/gromacs/mdrun/minimize.cpp
+@@ -49,6 +49,7 @@
+ #include <cmath>
+ #include <cstring>
+ #include <ctime>
++#include <limits>
+ 
+ #include <algorithm>
+ #include <vector>
diff --git a/gromacs.spec b/gromacs.spec
index d40bae7..be32011 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -8,7 +8,7 @@
 %endif
 Name:			gromacs
 Version:		2019.3
-Release:		3
+Release:		4
 Summary:		Fast, Free and Flexible Molecular Dynamics
 License:		GPLv2+ and ASL-2.0 and BSL-1.0 and MIT and LGPL-2.1
 URL:			http://www.gromacs.org
@@ -17,6 +17,7 @@ Source1:		https://ftp.gromacs.org/pub/manual/manual-%{version}.pdf
 Source2:		https://ftp.gromacs.org/regressiontests/regressiontests-%{version}.tar.gz
 Patch0:			gromacs-dssp-path.patch
 Patch1:			gromacs-issue-2366.patch
+Patch2:			gromacs-gcc11.patch
 BuildRequires:  	gcc-c++ cmake3 >= 3.4.3 openblas-devel fftw-devel gsl-devel hwloc
 BuildRequires:  	hwloc-devel libX11-devel lmfit-devel >= 6.0 environment-modules
 BuildRequires:          chrpath
@@ -149,6 +150,7 @@ This package single and double precision binaries and libraries.
 %setup -q %{?SOURCE2:-a 2} -n gromacs-%{version}%{?_rc}
 %patch0 -p1
 %patch1 -p1
+%patch2 -p1
 install -Dpm644 %{SOURCE1} ./serial/docs/manual/gromacs.pdf
 rm -r src/external/{fftpack,tng_io,lmfit}
 sed -i 's/set(_timeout [0-9]*)/set(_timeout 900)/' src/testutils/TestMacros.cmake
@@ -172,6 +174,7 @@ sed -i 's/set(_timeout [0-9]*)/set(_timeout 900)/' src/testutils/TestMacros.cmak
 %endif
 %global double -DGMX_DOUBLE:BOOL=ON
 %global mpi -DGMX_BUILD_MDRUN_ONLY:BOOL=ON -DGMX_MPI:BOOL=ON -DGMX_THREAD_MPI:BOOL=OFF -DGMX_DEFAULT_SUFFIX:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF
+. /etc/profile.d/modules.sh
 for p in '' _d ; do
   for mpi in '' mpich openmpi ; do
     test -n "${mpi}" && module load mpi/${mpi}-%{_arch}
@@ -234,6 +237,7 @@ echo "%{_libdir}/openmpi/lib" > %{buildroot}/etc/ld.so.conf.d/%{name}-openmpi-%{
 /sbin/ldconfig
 
 %check
+export OMPI_ALLOW_RUN_AS_ROOT=1
 . /etc/profile.d/modules.sh
 for p in '' _d ; do
   for mpi in '' mpich openmpi ; do
@@ -285,6 +289,10 @@ done
 %config(noreplace) /etc/ld.so.conf.d/%{name}-mpich-%{_arch}.conf
 
 %changelog
+* Mon Aug 07 2023 chenchen <chen_aka_jan@163.com> - 2019.3-4
+- fix build error due to gcc upgrade to gcc 12.3.4
+- add variable OMPI_ALLOW_RUN_AS_ROOT=1 for fix test error
+
 * Mon Dec 05 2022 Ge Wang <wangge20@h-partners.com> - 2019.3-3
 - Remove runpath