From: Roland Schulz <roland@utk.edu>
Date: Fri, 16 May 2014 20:23:11 +0000 (-0400)
Subject: Workaround for MemorySanitizer
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=4c5c666f9849ab01ca50459185edf3d530b61fb2;p=alexxy%2Fgromacs.git

Workaround for MemorySanitizer

MSan has false positives in qsort (Issue 54) and getlogin_r (83).

Change-Id: Ia63e918b59570e8dfb03222174bf83da24c6e219
---

diff --git a/src/gromacs/gmxlib/readinp.c b/src/gromacs/gmxlib/readinp.c
index 10a2c7cc36..ccc6ccea2b 100644
--- a/src/gromacs/gmxlib/readinp.c
+++ b/src/gromacs/gmxlib/readinp.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -49,6 +49,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/qsort_threadsafe.h"
 #include "gromacs/utility/smalloc.h"
 
 t_inpfile *read_inpfile(const char *fn, int *ninp,
@@ -238,7 +239,7 @@ static void sort_inp(int ninp, t_inpfile inp[])
             inp[i].count = mm++;
         }
     }
-    qsort(inp, ninp, (size_t)sizeof(inp[0]), inp_comp);
+    gmx_qsort(inp, ninp, (size_t)sizeof(inp[0]), inp_comp);
 }
 
 void write_inpfile(const char *fn, int ninp, t_inpfile inp[], gmx_bool bHaltOnUnknown,
diff --git a/src/gromacs/utility/sysinfo.cpp b/src/gromacs/utility/sysinfo.cpp
index cf7b6693ae..0166582298 100644
--- a/src/gromacs/utility/sysinfo.cpp
+++ b/src/gromacs/utility/sysinfo.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -121,7 +121,7 @@ int gmx_getusername(char *buf, size_t len)
     {
         return 0;
     }
-#elif defined(HAVE_UNISTD_H)
+#elif defined(HAVE_UNISTD_H) && !__has_feature(memory_sanitizer) //MSAN Issue 83
     if (!getlogin_r(buf, len))
     {
         buf[len-1] = '\0';