Merge branch 'develop' into features/xz

* develop: (85 commits)
  Make libxcb compile with gcc 4.9.
  disable parallel install for glib (found races)
  disable cairo-trace, which is incompatible with older libiberty.h.
  Fix LaunchMon on newer gcc versions.
  Simplify output redirection in spack.util.executable
  Allow completely empty config files.
  Update cmake package to use http in all URLs.
  Fix create, diy, edit, and repo commands to use multiple repos.
  Add namespace option to find command.
  Temporary fix: Clang is the default compiler on Mac OS X.
  Netcdf requires cmake >=2.8.12
  Mbedtls depends on cmake
  Update libtool to 2.4.6
  Update Julia to 0.4.3
  Make binutils build on OS X
  Add verbs and psm variants
  py-matplotlib: depend on freetype
  py-numpy: make blas/lapack optional dependencies
  qhull: apply patch to work with libc++'s standard library
  New package GNU tar
  ...

1 files changed, 395 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/libmonitor/libmonitorkrell-0001.patch b/var/spack/repos/builtin/packages/libmonitor/libmonitorkrell-0001.patch
new file mode 100644
index 0000000000..85d69595c0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmonitor/libmonitorkrell-0001.patch
@@ -0,0 +1,395 @@
+--- libmonitor-20130218/src/callback.c	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/callback.c	2013-02-18 10:34:17.839842826 -0800
+@@ -173,3 +173,18 @@
+     MONITOR_DEBUG1("(default callback)\n");
+     return 0;
+ }
++
++
++void __attribute__ ((weak))
++monitor_mpi_post_comm_rank(void)
++{
++    MONITOR_DEBUG1("(default callback)\n");
++}
++
++void __attribute__ ((weak))
++monitor_mpi_pcontrol(int level)
++{
++    MONITOR_DEBUG("(default callback) level = %d\n", level);
++} 
++
++
+--- libmonitor-20130218/src/main.c	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/main.c	2013-02-18 10:34:17.839842826 -0800
+@@ -230,6 +230,44 @@
+     monitor_fini_library_called = 1;
+ }
+ 
++/*
++ *  Internal monitor functions.
++ */
++
++struct monitor_thread_node * __attribute__ ((weak))
++monitor_get_tn(void)
++{
++    return &monitor_main_tn;
++}
++
++int __attribute__ ((weak))
++monitor_get_thread_num(void)
++{
++    return (0);
++}
++
++void __attribute__ ((weak))
++monitor_reset_thread_list(struct monitor_thread_node *main_tn)
++{
++    MONITOR_DEBUG1("(weak)\n");
++    return;
++}
++
++void __attribute__ ((weak))
++monitor_thread_release(void)
++{
++    MONITOR_DEBUG1("(weak)\n");
++    return;
++}
++
++void __attribute__ ((weak))
++monitor_thread_shootdown(void)
++{
++    MONITOR_DEBUG1("(weak)\n");
++    return;
++}
++
++
+ void
+ monitor_begin_process_fcn(void *user_data, int is_fork)
+ {
+@@ -625,12 +663,6 @@
+     return (monitor_main_tn.tn_user_data);
+ }
+ 
+-int __attribute__ ((weak))
+-monitor_get_thread_num(void)
+-{
+-    return (0);
+-}
+-
+ void * __attribute__ ((weak))
+ monitor_get_addr_thread_start(void)
+ {
+@@ -691,33 +723,3 @@
+     MONITOR_DEBUG1("(weak)\n");
+     return (FALSE);
+ }
+-
+-/*
+- *  Internal monitor functions.
+- */
+-struct monitor_thread_node * __attribute__ ((weak))
+-monitor_get_tn(void)
+-{
+-    return &monitor_main_tn;
+-}
+-
+-void __attribute__ ((weak))
+-monitor_reset_thread_list(struct monitor_thread_node *main_tn)
+-{
+-    MONITOR_DEBUG1("(weak)\n");
+-    return;
+-}
+-
+-void __attribute__ ((weak))
+-monitor_thread_release(void)
+-{
+-    MONITOR_DEBUG1("(weak)\n");
+-    return;
+-}
+-
+-void __attribute__ ((weak))
+-monitor_thread_shootdown(void)
+-{
+-    MONITOR_DEBUG1("(weak)\n");
+-    return;
+-}
+--- libmonitor-20130218/src/monitor.h	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/monitor.h	2013-02-18 10:34:17.840842821 -0800
+@@ -73,6 +73,11 @@
+ extern void monitor_fini_mpi(void);
+ extern void monitor_mpi_post_fini(void);
+ 
++extern void monitor_mpi_post_comm_rank(void);
++extern void monitor_mpi_pcontrol(int level);
++
++
++
+ /*
+  *  Monitor support functions.
+  */
+--- libmonitor-20130218/src/mpi_comm_c.c	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/mpi_comm_c.c	2013-02-18 10:34:17.878842622 -0800
+@@ -36,5 +36,8 @@
+     ret = (*real_mpi_comm_rank)(comm, rank);
+     monitor_set_mpi_size_rank(size, *rank);
+ 
++    monitor_mpi_post_comm_rank();
++
++
+     return (ret);
+ }
+--- libmonitor-20130218/src/mpi_comm_f0.c	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/mpi_comm_f0.c	2013-02-18 10:34:17.879842617 -0800
+@@ -34,4 +34,5 @@
+     (*real_mpi_comm_size)(comm, &size, ierror);
+     (*real_mpi_comm_rank)(comm, rank, ierror);
+     monitor_set_mpi_size_rank(size, *rank);
++    monitor_mpi_post_comm_rank();
+ }
+--- libmonitor-20130218/src/mpi_comm_f1.c	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/mpi_comm_f1.c	2013-02-18 10:34:17.880842612 -0800
+@@ -34,4 +34,5 @@
+     (*real_mpi_comm_size)(comm, &size, ierror);
+     (*real_mpi_comm_rank)(comm, rank, ierror);
+     monitor_set_mpi_size_rank(size, *rank);
++    monitor_mpi_post_comm_rank();
+ }
+--- libmonitor-20130218/src/mpi_comm_f2.c	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/mpi_comm_f2.c	2013-02-18 10:34:17.880842612 -0800
+@@ -34,4 +34,5 @@
+     (*real_mpi_comm_size)(comm, &size, ierror);
+     (*real_mpi_comm_rank)(comm, rank, ierror);
+     monitor_set_mpi_size_rank(size, *rank);
++    monitor_mpi_post_comm_rank();
+ }
+--- libmonitor-20130218/src/pmpi.c	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/pmpi.c	2013-02-18 10:34:17.881842607 -0800
+@@ -52,11 +52,15 @@
+ typedef int mpi_init_thread_fcn_t(int *, char ***, int, int *);
+ typedef int mpi_finalize_fcn_t(void);
+ typedef int mpi_comm_fcn_t(void *, int *);
++typedef int mpi_pcontrol_fcn_t(int );
++
+ 
+ typedef void f_mpi_init_fcn_t(int *);
+ typedef void f_mpi_init_thread_fcn_t(int *, int *, int *);
+ typedef void f_mpi_finalize_fcn_t(int *);
+ typedef void f_mpi_comm_fcn_t(int *, int *, int *);
++typedef int f_mpi_pcontrol_fcn_t(int );
++
+ 
+ static mpi_init_fcn_t    *real_pmpi_init = NULL;
+ static f_mpi_init_fcn_t  *real_pmpi_init_f0 = NULL;
+@@ -83,6 +87,12 @@
+ static f_mpi_comm_fcn_t  *real_pmpi_comm_rank_f1 = NULL;
+ static f_mpi_comm_fcn_t  *real_pmpi_comm_rank_f2 = NULL;
+ 
++static mpi_pcontrol_fcn_t    *real_pmpi_pcontrol = NULL;
++static f_mpi_pcontrol_fcn_t  *real_pmpi_pcontrol_f0 = NULL;
++static f_mpi_pcontrol_fcn_t  *real_pmpi_pcontrol_f1 = NULL;
++static f_mpi_pcontrol_fcn_t  *real_pmpi_pcontrol_f2 = NULL;
++
++
+ /*
+  *----------------------------------------------------------------------
+  *  PMPI_INIT OVERRIDE FUNCTIONS
+@@ -297,6 +307,7 @@
+     ret = (*real_pmpi_comm_size)(comm, &size);
+     ret = (*real_pmpi_comm_rank)(comm, rank);
+     monitor_set_mpi_size_rank(size, *rank);
++    monitor_mpi_post_comm_rank();
+ 
+     return (ret);
+ }
+@@ -308,7 +319,9 @@
+     MONITOR_GET_REAL_NAME_WRAP(rank_var, rank_fcn);	\
+     (*size_var)(comm, &size, ierror);			\
+     (*rank_var)(comm, rank, ierror);			\
+-    monitor_set_mpi_size_rank(size, *rank);
++    monitor_set_mpi_size_rank(size, *rank);             \
++    monitor_mpi_post_comm_rank();
++
+ 
+ /*
+  * In Fortran, MPI_Comm is always int.
+@@ -333,3 +346,48 @@
+     FORTRAN_COMM_RANK_BODY(real_pmpi_comm_size_f2, pmpi_comm_size__,
+ 			   real_pmpi_comm_rank_f2, pmpi_comm_rank__);
+ }
++
++
++/*
++ *----------------------------------------------------------------------
++ *  PMPI_PCONTROL OVERRIDE FUNCTIONS
++ *----------------------------------------------------------------------
++ */
++
++int
++MONITOR_WRAP_NAME(PMPI_Pcontrol)(int level)
++{
++    int ret;
++
++    MONITOR_DEBUG("level = %d\n", level);              \
++    MONITOR_GET_REAL_NAME_WRAP(real_pmpi_pcontrol, PMPI_Pcontrol);
++    ret = (*real_pmpi_pcontrol) (level) ;
++    monitor_mpi_pcontrol(level);
++
++    return (ret);
++}
++
++#define FORTRAN_PCONTROL_BODY(var_name, fcn_name)\
++    int ret;                                           \
++    MONITOR_DEBUG("level = %d\n", level);              \
++    MONITOR_GET_REAL_NAME_WRAP(var_name, fcn_name);    \
++    ret = (*var_name) (level) ;                        \
++    monitor_mpi_pcontrol(level);
++
++int
++MONITOR_WRAP_NAME(pmpi_pcontrol)(int level)
++{
++    FORTRAN_PCONTROL_BODY(real_pmpi_pcontrol_f0, pmpi_pcontrol);
++}
++
++int
++MONITOR_WRAP_NAME(pmpi_pcontrol_)(int level)
++{
++    FORTRAN_PCONTROL_BODY(real_pmpi_pcontrol_f1, pmpi_pcontrol_);
++}
++
++int
++MONITOR_WRAP_NAME(pmpi_pcontrol__)(int level)
++{
++    FORTRAN_PCONTROL_BODY(real_pmpi_pcontrol_f2, pmpi_pcontrol__);
++}
+--- libmonitor-20130218/src/mpi_pcontrol_c.c	1969-12-31 16:00:00.000000000 -0800
++++ libmonitor-20130218-fixes/src/mpi_pcontrol_c.c	2013-02-18 10:34:17.882842602 -0800
+@@ -0,0 +1,30 @@
++/*
++ *  Override MPI_Pcontrol in C/C++.
++ *
++ *  
++ */
++
++#include "config.h"
++#include "common.h"
++#include "monitor.h"
++
++typedef int mpi_pcontrol_fcn_t(int level);
++#ifdef MONITOR_STATIC
++extern mpi_pcontrol_fcn_t  __real_MPI_Pcontrol;
++#endif
++static mpi_pcontrol_fcn_t  *real_mpi_pcontrol = NULL;
++
++int
++MONITOR_WRAP_NAME(MPI_Pcontrol)(int level)
++{
++    int ret, count;
++
++    MONITOR_DEBUG("level = %d\n", level);               \
++
++    MONITOR_GET_REAL_NAME_WRAP(real_mpi_pcontrol, MPI_Pcontrol);
++    ret = (*real_mpi_pcontrol)(level);
++    monitor_mpi_pcontrol(level);
++
++
++    return (ret);
++}
+--- libmonitor-20130218/src/mpi_pcontrol_f0.c	1969-12-31 16:00:00.000000000 -0800
++++ libmonitor-20130218-fixes/src/mpi_pcontrol_f0.c	2013-02-18 10:34:17.882842602 -0800
+@@ -0,0 +1,24 @@
++/*
++ *  Override mpi_pcontrol in Fortran.
++ *
++ */
++
++#include "config.h"
++#include "common.h"
++#include "monitor.h"
++
++typedef void mpi_pcontrol_fcn_t(int level);
++#ifdef MONITOR_STATIC
++extern mpi_pcontrol_fcn_t  __real_mpi_pcontrol;
++#endif
++static mpi_pcontrol_fcn_t  *real_mpi_pcontrol = NULL;
++
++int
++MONITOR_WRAP_NAME(mpi_pcontrol)(int level)
++{
++    int count;
++
++    MONITOR_DEBUG1("\n");
++    MONITOR_GET_REAL_NAME_WRAP(real_mpi_pcontrol, mpi_pcontrol);
++    (*real_mpi_pcontrol)(level);
++}
+--- libmonitor-20130218/src/mpi_pcontrol_f1.c	1969-12-31 16:00:00.000000000 -0800
++++ libmonitor-20130218-fixes/src/mpi_pcontrol_f1.c	2013-02-18 10:34:17.883842597 -0800
+@@ -0,0 +1,24 @@
++/*
++ *  Override mpi_pcontrol_ in Fortran.
++ *
++ */
++
++#include "config.h"
++#include "common.h"
++#include "monitor.h"
++
++typedef void mpi_pcontrol_fcn_t(int level);
++#ifdef MONITOR_STATIC
++extern mpi_pcontrol_fcn_t  __real_mpi_pcontrol_;
++#endif
++static mpi_pcontrol_fcn_t  *real_mpi_pcontrol = NULL;
++
++int
++MONITOR_WRAP_NAME(mpi_pcontrol_)(int level)
++{
++    int count;
++
++    MONITOR_DEBUG1("\n");
++    MONITOR_GET_REAL_NAME_WRAP(real_mpi_pcontrol, mpi_pcontrol_);
++    (*real_mpi_pcontrol)(level);
++}
+--- libmonitor-20130218/src/mpi_pcontrol_f2.c	1969-12-31 16:00:00.000000000 -0800
++++ libmonitor-20130218-fixes/src/mpi_pcontrol_f2.c	2013-02-18 10:34:17.883842597 -0800
+@@ -0,0 +1,24 @@
++/*
++ *  Override mpi_pcontrol__ in Fortran.
++ *
++ */
++
++#include "config.h"
++#include "common.h"
++#include "monitor.h"
++
++typedef void mpi_pcontrol_fcn_t(int level);
++#ifdef MONITOR_STATIC
++extern mpi_pcontrol_fcn_t  __real_mpi_pcontrol__;
++#endif
++static mpi_pcontrol_fcn_t  *real_mpi_pcontrol = NULL;
++
++int
++MONITOR_WRAP_NAME(mpi_pcontrol__)(int level)
++{
++    int count;
++
++    MONITOR_DEBUG1("\n");
++    MONITOR_GET_REAL_NAME_WRAP(real_mpi_pcontrol, mpi_pcontrol__);
++    (*real_mpi_pcontrol)(level);
++}
+--- libmonitor-20130218/src/Makefile.am	2013-02-17 23:08:32.000000000 -0800
++++ libmonitor-20130218-fixes/src/Makefile.am	2013-02-18 10:34:17.931842343 -0800
+@@ -38,10 +38,11 @@
+ MONITOR_THREAD_FILES = pthread.c
+ MONITOR_SCRIPT_FILES = monitor-link monitor-run
+ MONITOR_MPI_FILES =  \
+-	mpi_init_c.c  mpi_init_thread_c.c  mpi_final_c.c  mpi_comm_c.c   \
+-	mpi_init_f0.c mpi_init_thread_f0.c mpi_final_f0.c mpi_comm_f0.c  \
+-	mpi_init_f1.c mpi_init_thread_f1.c mpi_final_f1.c mpi_comm_f1.c  \
+-	mpi_init_f2.c mpi_init_thread_f2.c mpi_final_f2.c mpi_comm_f2.c
++       mpi_init_c.c  mpi_init_thread_c.c  mpi_final_c.c  mpi_comm_c.c mpi_pcontrol_c.c  \
++       mpi_init_f0.c mpi_init_thread_f0.c mpi_final_f0.c mpi_comm_f0.c mpi_pcontrol_f0.c \
++       mpi_init_f1.c mpi_init_thread_f1.c mpi_final_f1.c mpi_comm_f1.c mpi_pcontrol_f1.c \
++       mpi_init_f2.c mpi_init_thread_f2.c mpi_final_f2.c mpi_comm_f2.c mpi_pcontrol_f2.c
++
+ 
+ include_HEADERS = monitor.h
+ bin_SCRIPTS =