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Harry M. Greenblatt

24 May 2010 24 May '10

11:56 a.m.

BS"D Dear All, We had the phenix 1.6.1 GUI running on a fedora core 12 machine; it was thought, for different reasons, that a kernel upgrade would address certain issues unrelated to phenix. The machine is now running 2.6.32.12-115.fc12 (64 bit) and phenix now gives a segmentation fault. Any suggestions? Thanks Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology [email protected] Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

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Nathaniel Echols

24 May 24 May

2:15 p.m.

On Mon, May 24, 2010 at 4:56 AM, Harry M. Greenblatt < [email protected]> wrote:

We had the phenix 1.6.1 GUI running on a fedora core 12 machine; it was thought, for different reasons, that a kernel upgrade would address certain issues unrelated to phenix.

The machine is now running 2.6.32.12-115.fc12 (64 bit) and phenix now gives a segmentation fault. Any suggestions?

I'm afraid you're probably going to need to compile from source to get around this: https://www.phenix-online.org/download/phenix/source/ It takes several hours to build, so if you have multiple processors/cores, we recommend adding "--nproc=X" (were X = number of processes to run simultaneously) to the install command to speed it up. Just curious - did you upgrade the kernel from scratch, or use a fedora package, and does anything else break, or just Phenix? I've seen kernel upgrades cause havoc before, but usually all sorts of programs stop working, not just one. -Nat

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jens j birktoft

1 Jun 1 Jun

2:18 p.m.

Hi all, Trying to install nightly release 421 fails, giving the following error OS is 2.6.32.12-115.fc12.x86_64 Installation of previous versions have worked without problems, no changes (kernel updates etc) has been made to the OS Any suggestions will be appreciated Jens # ./install ========================================================================== PHENIX Installation version: dev release tag: 421 machine type: intel-linux-2.6-x86_64 OS version: linux user shell: /bin/bash destination: /usr/local ========================================================================== Installing from binary bundle ========================================================================== bundle file: bundle-dev-421-intel-linux-2.6-x86_64.tar.gz PHENIX installation source directory set to: /My_Downloads/PHENIX/phenix-installer-dev-421_64bit PHENIX installation target directory set to: /usr/local/phenix-dev-421 PHENIX installation build directory set to: /build/intel-linux-2.6-x86_64 PHENIX temporary build directory set to: build-binary/intel-linux-2.6-x86_64/jens-HPE180/tmp PHENIX installation log directory set to: build-binary/intel-linux-2.6-x86_64/jens-HPE180/log making directory: /usr/local/phenix-dev-421 making directory: /build/intel-linux-2.6-x86_64 installing binary components removing existing files in build-binary/intel-linux-2.6-x86_64/jens-HPE180/tmp/binary finding installed versions finding binary versions no pre-existing binary components detected installing new binary package setting environment configuring PHENIX components /My_Downloads/PHENIX/phenix-installer-dev-421_64bit/bin/install-from-binary: line 347: 3735 Segmentation fault (core dumped) $PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py --current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS >> $PHENIX_LOG/binary.log 2>&1 Error configuring: see /My_Downloads/PHENIX/phenix-installer-dev-421_64bit/build-binary/intel-linux-2.6-x86_64/jens-HPE180/log/binary.log for details

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Nathaniel Echols

2:26 p.m.

On Tue, Jun 1, 2010 at 7:18 AM, jens j birktoft wrote:

Hi all,

Trying to install nightly release 421 fails, giving the following error

OS is 2.6.32.12-115.fc12.x86_64

Installation of previous versions have worked without problems, no changes (kernel updates etc) has been made to the OS

. . . /My_Downloads/PHENIX/phenix-installer-dev-421_64bit/bin/install-from-binary: line 347: 3735 Segmentation fault (core dumped) $PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py

Again, you'll need to try installing from source. I'm a little worried that we've switched back to the older build system and we're still seeing this error, however. I take it you're running Fedora Core 12? -Nat

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jens j birktoft

3:57 p.m.

Nat: Thanks, Yes, I am running FC12. For what ever it is worth, the installation works fine with FC11 (32 BIT) Any plans to restore the previous installation procedure. Otherwise the regular, frequent updating becomes a much more tedious and time consuming process. Best, Jens On Tue, Jun 1, 2010 at 10:26, Nathaniel Echols wrote:

On Tue, Jun 1, 2010 at 7:18 AM, jens j birktoft wrote:

...
Hi all,

Trying to install nightly release 421 fails, giving the following error

OS is 2.6.32.12-115.fc12.x86_64

Installation of previous versions have worked without problems, no changes (kernel updates etc) has been made to the OS

. . .

/My_Downloads/PHENIX/phenix-installer-dev-421_64bit/bin/install-from-binary: line 347: 3735 Segmentation fault (core dumped) $PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py

Again, you'll need to try installing from source. I'm a little worried that we've switched back to the older build system and we're still seeing this error, however. I take it you're running Fedora Core 12?

-Nat

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Jens J. Birktoft e-mail: [email protected] slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057 for ALL calls

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Nathaniel Echols

4:32 p.m.

On Tue, Jun 1, 2010 at 8:57 AM, jens j birktoft wrote:

Thanks, Yes, I am running FC12. For what ever it is worth, the installation works fine with FC11 (32 BIT)

Any plans to restore the previous installation procedure. Otherwise the regular, frequent updating becomes a much more tedious and time consuming process.

This *was* the previous installation procedure - we switched back to the current build machine (running Fedora Core 3) because building the installers on FC 8 resulted in many more reports of segmentation faults. I guess we may need to start building multiple x86_64 installers, but that'll have to wait until at least next week. -Nat

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jens j birktoft

4:43 p.m.

Sounds good - thanks - Jens On Tue, Jun 1, 2010 at 12:32, Nathaniel Echols wrote:

On Tue, Jun 1, 2010 at 8:57 AM, jens j birktoft wrote:

...
Thanks, Yes, I am running FC12. For what ever it is worth, the installation works fine with FC11 (32 BIT)

Any plans to restore the previous installation procedure. Otherwise the regular, frequent updating becomes a much more tedious and time consuming process.

This *was* the previous installation procedure - we switched back to the current build machine (running Fedora Core 3) because building the installers on FC 8 resulted in many more reports of segmentation faults. I guess we may need to start building multiple x86_64 installers, but that'll have to wait until at least next week.

-Nat

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Jens J. Birktoft e-mail: [email protected] slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 Phone: 212-749-5057 for ALL calls

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Harry M. Greenblatt
jens j birktoft
jens j birktoft
Nathaniel Echols