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Bug#770738: marked as done (unblock: nwchem/6.5+r26243-4)

Your message dated Sat, 29 Nov 2014 10:33:35 +0100
with message-id <547992EF.3030802@thykier.net>
and subject line Re: Bug#770738: unblock: nwchem/6.5+r26243-4
has caused the Debian Bug report #770738,
regarding unblock: nwchem/6.5+r26243-4
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
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immediately.)


-- 
770738: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=770738
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock

Please unblock package nwchem

This fixes a FTBFS bug on a previously uncompiled architecture (arm64),
a serious miscompile which leads to SIGILL on some amd64 CPUs, and it
reintroduces a Debian-specific patch which makes nwchem find essential
data files at runtime. 

The last one can be worked-around by setting an environment variable or
setting up a configuration file, but it should really just-work, as it
did for jessie.


Michael

unblock nwchem/6.5+r26243-4

-- System Information:
Debian Release: jessie/sid
  APT prefers testing-updates
  APT policy: (500, 'testing-updates'), (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.16-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

diff -Nru nwchem-6.5+r26243/debian/changelog nwchem-6.5+r26243/debian/changelog
--- nwchem-6.5+r26243/debian/changelog	2014-10-12 00:22:00.000000000 +0200
+++ nwchem-6.5+r26243/debian/changelog	2014-11-23 17:36:00.000000000 +0100
@@ -1,3 +1,20 @@
+nwchem (6.5+r26243-4) unstable; urgency=medium
+
+  * debian/patches/02_makefile_flags.patch: Patch updated, to remove -m64 from
+    compiler flags on arm64 (Closes: #769525).
+
+ -- Michael Banck <mbanck@debian.org>  Sun, 23 Nov 2014 17:35:50 +0100
+
+nwchem (6.5+r26243-3) unstable; urgency=medium
+
+  * debian/patches/02_makefile_flags.patch: Patch updated to remove additions
+    to $(FOPTIMIZE) which are not applicable to the baseline amd64
+    architecture (Closes: #767481).
+  * debian/patches/01_hardcode_basis-sets_location.patch: Reintroduced patch,
+    updated (Closes: #769297).
+
+ -- Michael Banck <mbanck@debian.org>  Thu, 13 Nov 2014 14:01:47 +0100
+
 nwchem (6.5+r26243-2) unstable; urgency=medium
 
   * debian/patches/14_fix_ga_download.patch: Updated to surpress unnecessary
diff -Nru nwchem-6.5+r26243/debian/patches/01_hardcode_basis-sets_location.patch nwchem-6.5+r26243/debian/patches/01_hardcode_basis-sets_location.patch
--- nwchem-6.5+r26243/debian/patches/01_hardcode_basis-sets_location.patch	1970-01-01 01:00:00.000000000 +0100
+++ nwchem-6.5+r26243/debian/patches/01_hardcode_basis-sets_location.patch	2014-11-12 23:53:21.000000000 +0100
@@ -0,0 +1,33 @@
+Index: nwchem-6.5+r26243/src/basis/bas_input.F
+===================================================================
+--- nwchem-6.5+r26243.orig/src/basis/bas_input.F
++++ nwchem-6.5+r26243/src/basis/bas_input.F
+@@ -1180,12 +1180,11 @@ c
+       noslash=.false.
+       calls = calls + 1
+       if (debug) write(luout,*)' calls:calls: ',calls
+-      call util_nwchem_srcdir(compiled_name)
++c     call util_nwchem_srcdir(compiled_name)
+ c
+ c     add here basis/libraries bit
+ c
+-      compiled_name=compiled_name(1:inp_strlen(compiled_name))
+-     $     //"/basis/libraries/"
++      compiled_name="/usr/share/nwchem/libraries/"
+ *
+ * order of precedence for choosing name
+ * 1) value of NWCHEM_BASIS_LIBRARY environment variable
+Index: nwchem-6.5+r26243/src/nwpw/libraryps/nwpw_libfile.F
+===================================================================
+--- nwchem-6.5+r26243.orig/src/nwpw/libraryps/nwpw_libfile.F
++++ nwchem-6.5+r26243/src/nwpw/libraryps/nwpw_libfile.F
+@@ -118,8 +118,7 @@ c    &NWPW_LIBRARY
+ c
+ c     add here nwpw/libraryps bit
+ c
+-      libname=libname(1:inp_strlen(libname))
+-     &     //"/nwpw/libraryps/"
++      libname="/usr/share/nwchem/libraryps/"
+       if (util_find_dir(libname)) then
+          goto 99
+       else
diff -Nru nwchem-6.5+r26243/debian/patches/02_makefile_flags.patch nwchem-6.5+r26243/debian/patches/02_makefile_flags.patch
--- nwchem-6.5+r26243/debian/patches/02_makefile_flags.patch	2014-09-28 12:35:42.000000000 +0200
+++ nwchem-6.5+r26243/debian/patches/02_makefile_flags.patch	2014-11-23 17:35:47.000000000 +0100
@@ -1,7 +1,7 @@
-Index: nwchem-6.5/src/config/makefile.h
+Index: nwchem-6.5+r26243/src/config/makefile.h
 ===================================================================
---- nwchem-6.5.orig/src/config/makefile.h
-+++ nwchem-6.5/src/config/makefile.h
+--- nwchem-6.5+r26243.orig/src/config/makefile.h
++++ nwchem-6.5+r26243/src/config/makefile.h
 @@ -1384,7 +1384,7 @@ endif
  endif
  
@@ -54,10 +54,50 @@
    _G77V33= $(shell g77 -v  2>&1|egrep spec|head -n 1|awk ' /3.3/  {print "Y"}')
  
        ifeq ($(FC),g77)
-Index: nwchem-6.5/src/peigs/DEFS
+@@ -1758,13 +1758,6 @@
+       endif
+       FOPTIMIZE  = -O2 
+       ifeq ($(_FC),gfortran)
+-       ifeq ($(_CPU),aarch64)
+-         DONTHAVEM64OPT=Y
+-       endif
+-       ifneq ($(DONTHAVEM64OPT),Y)
+-         FOPTIONS   = -m64
+-         COPTIONS   = -m64
+-       endif
+         COPTIONS += -Wall
+         FOPTIONS   += -ffast-math #-Wunused  
+         FOPTIMIZE  += -ffast-math -Wuninitialized
+@@ -2125,25 +2118,12 @@
+         endif
+ 	    LINK.f = $(FC)  $(LDFLAGS) 
+         FOPTIMIZE  += -O3 
+-        FOPTIMIZE  += -mfpmath=sse -ffast-math
+-        FOPTIMIZE  += -fprefetch-loop-arrays #-ftree-loop-linear
+         FDEBUG += -g -O 
+         ifdef USE_F2C
+ #possible segv with use of zdotc (e.g. with GOTO BLAS)
+ #http://gcc.gnu.org/bugzilla/show_bug.cgi?id=20178
+           FOPTIONS +=  -ff2c -fno-second-underscore
+         endif
+-        ifeq ($(GNU_GE_4_6),true) 
+-          FOPTIMIZE += -march=native -mtune=native
+-        else
+-        ifeq ($(_GOT3DNOW),Y) 
+-#we guess its an opteron
+-          FOPTIMIZE += -march=opteron -mtune=opteron
+-        else
+-#we guess its a nocona em64t
+-          FOPTIMIZE += -march=nocona -mtune=nocona
+-        endif
+-        endif
+ #        FVECTORIZE  += -ftree-vectorize -ftree-vectorizer-verbose=1
+       endif
+       ifeq ($(_FC),crayftn)
+Index: nwchem-6.5+r26243/src/peigs/DEFS
 ===================================================================
---- nwchem-6.5.orig/src/peigs/DEFS
-+++ nwchem-6.5/src/peigs/DEFS
+--- nwchem-6.5+r26243.orig/src/peigs/DEFS
++++ nwchem-6.5+r26243/src/peigs/DEFS
 @@ -68,7 +68,7 @@ peigs_FC = $(FC) $(FOPTIONS) $(FOPTIMIZE
  # this is needed because -DCRAY-T3E cannot be a macro definition it should be -DCRAY_T3E
  #
diff -Nru nwchem-6.5+r26243/debian/patches/series nwchem-6.5+r26243/debian/patches/series
--- nwchem-6.5+r26243/debian/patches/series	2014-10-10 17:44:01.000000000 +0200
+++ nwchem-6.5+r26243/debian/patches/series	2014-11-12 16:07:57.000000000 +0100
@@ -1,3 +1,4 @@
+01_hardcode_basis-sets_location.patch
 02_makefile_flags.patch
 03_hurd-i386_define_path_max.patch
 04_show_testsuite_diff_output.patch

--- End Message ---
--- Begin Message --- 
On 2014-11-23 19:21, Michael Banck wrote:
> Package: release.debian.org
> Severity: normal
> User: release.debian.org@packages.debian.org
> Usertags: unblock
> 
> Please unblock package nwchem
> 
> This fixes a FTBFS bug on a previously uncompiled architecture (arm64),
> a serious miscompile which leads to SIGILL on some amd64 CPUs, and it
> reintroduces a Debian-specific patch which makes nwchem find essential
> data files at runtime. 
> 
> The last one can be worked-around by setting an environment variable or
> setting up a configuration file, but it should really just-work, as it
> did for jessie.
> 
> 
> Michael
> 
> unblock nwchem/6.5+r26243-4
> 
> [...]

Unblocked, thanks.

~Niels

--- End Message ---
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