From owner-freebsd-ports-bugs@FreeBSD.ORG Thu Jul 6 12:21:08 2006 Return-Path: X-Original-To: freebsd-ports-bugs@hub.freebsd.org Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id BB06116A4E8 for ; Thu, 6 Jul 2006 12:21:08 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 24D2343D9F for ; Thu, 6 Jul 2006 12:20:31 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.4/8.13.4) with ESMTP id k66CKJrm083127 for ; Thu, 6 Jul 2006 12:20:19 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.4/8.13.4/Submit) id k66CKJUK083124; Thu, 6 Jul 2006 12:20:19 GMT (envelope-from gnats) Resent-Date: Thu, 6 Jul 2006 12:20:19 GMT Resent-Message-Id: <200607061220.k66CKJUK083124@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Davide Cittaro Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 37ECE16A4E0 for ; Thu, 6 Jul 2006 12:15:56 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [216.136.204.117]) by mx1.FreeBSD.org (Postfix) with ESMTP id 44FB443D72 for ; Thu, 6 Jul 2006 12:15:51 +0000 (GMT) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.13.1/8.13.1) with ESMTP id k66CFp3i054294 for ; Thu, 6 Jul 2006 12:15:51 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.13.1/8.13.1/Submit) id k66CFpUu054292; Thu, 6 Jul 2006 12:15:51 GMT (envelope-from nobody) Message-Id: <200607061215.k66CFpUu054292@www.freebsd.org> Date: Thu, 6 Jul 2006 12:15:51 GMT From: Davide Cittaro To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-2.3 Cc: Subject: ports/99839: [sysutils/sge] patch to ensure correct support of berkeleydb spooling in sun grid engine X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 06 Jul 2006 12:21:08 -0000 >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: