Date: Thu, 6 Jul 2006 12:15:51 GMT From: Davide Cittaro <daweonline@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/99839: [sysutils/sge] patch to ensure correct support of berkeleydb spooling in sun grid engine Message-ID: <200607061215.k66CFpUu054292@www.freebsd.org> Resent-Message-ID: <200607061220.k66CKJUK083124@freefall.freebsd.org>
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>Number: 99839
>Category: ports
>Synopsis: [sysutils/sge] patch to ensure correct support of berkeleydb spooling in sun grid engine
>Confidential: no
>Severity: non-critical
>Priority: medium
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: sw-bug
>Submitter-Id: current-users
>Arrival-Date: Thu Jul 06 12:20:19 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator: Davide Cittaro
>Release: 5.4
>Organization:
IFOM
>Environment:
FreeBSD host12.bioinfo3.servers.ifom-ieo-campus.it 5.4-RELEASE-p12 FreeBSD 5.4-RELEASE-p12 #0: Thu Mar 2 12:57:38 CET 2006 root@master.bioinfo3.servers.ifom-ieo-campus.it:/usr/obj/usr/src/sys/ALCATRAZ i386
>Description:
If one installs sun grid engine 6 (6.0u7 at time of writing) with ports (sysutils/sge), it is impossible to use berkeleydb support for spooling database, as one gets this error during the installation:
creating directory: /usr/local/sge/campus/spool/spooldb
Dumping bootstrapping information
Initializing spooling database
critical error: Profiling array is not initialized!
Abort trap (core dumped)
Command failed: ./utilbin/fbsd-i386/spoolinit berkeleydb libspoolb /usr/local/sge/campus/spool/spooldb init
Probably a permission problem. Please check file access permissions.
Check read/write permission. Check if SGE daemons are running.
So that one has to use only classic spooling method.
>How-To-Repeat:
Install sge with BDB support
cd /usr/ports/sysutils/sge
make WITH_BDB=yes install
After installation move to $SGE_ROOT directory (default /usr/local/sge) and install the qmaster:
./install_qmaster
The error is given during the assisted installation, once choosen the spooling directory
>Fix:
A way to fix this is adding "-export-dynamic" value to LFLAGS and SHARED_LFLAGS in aimk file (gridengine/source/aimk). Since aimk is patched if sge is installed with ports, I suggest to modify the patch-aimk file (/usr/ports/sysutils/sge/files/patch-aimk) with the one pasted below:
$ cat patch-aimk.new
--- aimk.orig Tue Oct 25 19:48:15 2005
+++ aimk Thu Jul 6 13:46:28 2006
@@ -397,7 +397,7 @@
if ( $?SGE_INPUT_CFLAGS ) then
set INP_CFLAGS = "$SGE_INPUT_CFLAGS"
else
- set INP_CFLAGS = ""
+ set INP_CFLAGS = "%%CFLAGS%%"
endif
# Default build targets for which we have seperate make files
@@ -437,7 +437,7 @@
set DRMAA_TARGET = "ALL"
set PROTECTED = 0
-set LFLAGS = "-L."
+set LFLAGS = "-export-dynamic -L."
set XLFLAGS = ""
set XLIBS = ""
set LIBS = "-lm -lpthread"
@@ -453,7 +453,7 @@
set SHAREDEXT = ".so"
set SHAREDLD = ""
set SHARED_CFLAGS = ""
-set SHARED_LFLAGS = ""
+set SHARED_LFLAGS = "-export-dynamic"
# Flags for man page creation, copyright stuff and adoc
set BUILDMAN = 0
@@ -1180,8 +1180,8 @@
set MAKE = gmake
set OFLAG = "-O"
set ARFLAGS = rcv
- set CC = gcc
- set CXX = g++
+ set CC = %%CC%%
+ set CXX = %%CXX%%++
set DLLIB = ""
set DEPEND_FLAGS = "$CFLAGS $XMTINCD"
set PTHRDSFLAGS = "-D_REENTRANT -D__USE_REENTRANT"
@@ -1200,7 +1200,7 @@
set XLFLAGS = "$XLIBD"
set XLIBS = " -Xlinker -lXm -Xlinker -Bdynamic -lXpm -lXt -lXext -lX11 -lSM -lICE -lXp"
set RM = "rm -f"
- set JAVA_ARCH = ""
+ set JAVA_ARCH = "freebsd"
breaksw
case NETBSD_*:
>Release-Note:
>Audit-Trail:
>Unformatted:
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