Hello SGE Experts,

I have unzipped sge 8.1.9.tar file and coppied into my /home went to ...../source folder done ./scripts/bootstrap.sh Status: "Build successful.....Run ./aimk" after ./aimk warning [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 with multiple errors like 1.error: package junit.framework does not exist

2. error: cannot find symbol [java] [javac] public static Test

suite() { 3.fail("Unable to modify user qtask file") 4.fail("Unable to create job script"); ...etc.

Kindly advise the needful

Looking forward to hear from you

Regards

-- Himanshu Joshi M.Tech. Cognitive & Neuroscience. Ph.D Scholar, Department of Psychiatry NIMHANS, Bangalore Publications <​https://scholar.google.co.in/citations?hl=en&user=OspDsGUAAAAJ&view_op=list_works&gmla=AJsN-F4EvpCnES94r26jSpcDQFnN_-rSpEtp0PNdwObxCjniNpjkL55yPooOzK6epx6bHLvPuwJ2LIL3Wgkvxn4xeZXy5Wh0NpiR4E_Ebq88a1jaCS4r5q14b_4jCaeeDct8aeK15Bxr> Multimodal Brain Image Analysis Laboratory <​http://mbial.weebly.com/himanshu-joshi.html>

Hello,

we experienced a problem on RHEL/CentOS 6 machines with qlogin/qrsh via the builtin starter. The job seems to be scheduled and started fine, but for some reason the shell at the end won't start and the job ends with a commlib error:

$ qlogin -verbose -q queue@host Your job 998 ("QLOGIN") has been submitted waiting for interactive job to be scheduled ... Your interactive job 998 has been successfully scheduled. Establishing builtin session to host exechost.f.q.d.n ... error: commlib error: got read error (closing "exechost.f.q.d.n/shepherd_ijs/2")

Tracing through the execd on the destination machine showed that the execle() call for the shell failed with EFAULT:

write(4, "07/09/2013 08:30:44 [50449:30912]: execle(/bin/bash, -bash, NULL,

env)\n", 71) = 71

execve("/bin/bash", -bash?, ["SHELL=/bin/bash", "HOME=/home/username",

"TERM=xterm", "LOGNAME=username", "PATH=/bin:/usr/bin", 0x7fffffffffff]) = -1 EFAULT

After some digging it looks like the environment array the funtion start_qlogin_job() generates isn't properly ended with a NULL pointer any more (like it was in the SGE 6.2u5 source).

The attached trivial patch fixed our problems.

Regards, Thomas Mainka

-- Thomas Mainka science+computing ag System Administration Hagellocher Weg 73 mail: t.mainka@… 72070 Tuebingen, Germany tel.: +49 7071 9457 472 www.science-computing.de -- Vorstandsvorsitzender/Chairman? of the board of management: Gerd-Lothar Leonhart Vorstand/Board? of Management: Dr. Bernd Finkbeiner, Michael Heinrichs, Dr. Arno Steitz, Dr. Ingrid Zech Vorsitzender des Aufsichtsrats/ Chairman of the Supervisory Board: Philippe Miltin Sitz/Registered? Office: Tuebingen Registergericht/Registration? Court: Stuttgart Registernummer/Commercial? Register No.: HRB 382196

sge-builtin_starter.patch​

Adam DeConinck <adeconinck@rsystemsinc.com> writes:

> On 8/10/2011 9:07 AM, Dave Love wrote:
>> Adam DeConinck <adeconinck@rsystemsinc.com> writes:
>>
>>> Downloaded gridenine-8.0.0a-2.src.rpm from
>>> http://arc.liv.ac.uk/downloads/SGE/releases/8.0.0a/.  Server is a test
>>> machine running RHEL 6.1 x86_64.  Installed the src rpm (as root), and
>>> confirmed that all dependencies were in place, then ran "rpmbuild -bb
>>> --without java gridengine.spec"
>>>
>>> Build failed with the following output:
>>>
>>> echo libXmt.a
>>> libXmt.a
>>> gcc -c -DALLOW_COLUMN_RESIZE -DDRAW_RESIZE_SHADOW -I../Xmt310
>>> -DSGE_ARCH_STRING=\"lx-amd64\" -O3 -Wall -Wstrict-prototypes -DUSE_POLL
>>> -DLINUX -DLINUXAMD64 -DLINUXAMD64 -D_GNU_SOURCE -DGETHO
>>> gcc -c -DALLOW_COLUMN_RESIZE -DDRAW_RESIZE_SHADOW -I../Xmt310
>>> -DSGE_ARCH_STRING=\"lx-amd64\" -O3 -Wall -Wstrict-prototypes -DUSE_POLL
>>> -DLINUX -DLINUXAMD64 -DLINUXAMD64 -D_GNU_SOURCE -DGETHO
>>> gcc -c -DALLOW_COLUMN_RESIZE -DDRAW_RESIZE_SHADOW -I../Xmt310
>>> -DSGE_ARCH_STRING=\"lx-amd64\" -O3 -Wall -Wstrict-prototypes -DUSE_POLL
>>> -DLINUX -DLINUXAMD64 -DLINUXAMD64 -D_GNU_SOURCE -DGETHO
>>> In file included from /usr/include/X11/Xft/Xft.h:39,
>>>                  from /usr/include/Xm/TextFP.h:47,
>>>                  from ../Xbae/CellP.h:35,
>>>                  from ../Xbae/Cell.c:28:
>>> /usr/include/ft2build.h:56:38: error: freetype/config/ftheader.h: No
>>> such file or directory

This definitely looks like a system problem, but I don't understand the
problem on RH6 yet.  On RH5

  $ cc -E - >/dev/null <<+
  #include <Xm/TextFP.h>
  +

works, but on RH6, it complains about the file, as above and, in fact,
including just Xft.h fails as above.

I see that the EPEL gridengine package has added

  export SGE_INPUT_CFLAGS="$RPM_OPT_FLAGS -I%{_includedir}/freetype2"

to the spec %build section before running aimk, but I think I'll put a
workaround in aimk -- patch available shortly.

Thanks for the report.