Hi, I was trying to install the 32 bit Phenix-dev-782 or the official release 1.7.1-743 onto a virtual ubuntu 10.04 32-bit machine. Both of them failed with this error: /bin/tar: ./build/intel-linux-2.6/base/bin/wx-config: Cannot create symlink to `/net/longnose/scratch2/phenix/phenix-dev-782/build/intel-linux-2.6/base/lib/wx/config/gtk2-ansi-release-2.8': Operation not supported /bin/tar: Exiting with failure status due to previous errors /mnt/hgfs/windubuntu/phenix-installer-dev-782/bin/install-from-binary: 352: /usr/local/phenix-dev-782/build/intel-linux-2.6/base/bin/python: not found Any comments? Thanks. Daqi Tu
On Fri, Jun 10, 2011 at 2:45 PM, Daqi Tu
I was trying to install the 32 bit Phenix-dev-782 or the official release 1.7.1-743 onto a virtual ubuntu 10.04 32-bit machine. Both of them failed with this error:
/bin/tar: ./build/intel-linux-2.6/base/bin/wx-config: Cannot create symlink to `/net/longnose/scratch2/phenix/phenix-dev-782/build/intel-linux-2.6/base/lib/wx/config/gtk2-ansi-release-2.8': Operation not supported /bin/tar: Exiting with failure status due to previous errors /mnt/hgfs/windubuntu/phenix-installer-dev-782/bin/install-from-binary: 352: /usr/local/phenix-dev-782/build/intel-linux-2.6/base/bin/python: not found
The symlinks to our filesystems that hang around are a known problem, but they very rarely actually break the installer. I tried dev-782 on a 64-bit Ubuntu 10.04 system without these filesystems - both the 32-bit and 64-bit FC3 installers - and it worked as expected, so it's probably not an issue with the installer itself. After some quick Googling*, my best guess is that there is some problem with the local filesystems, particularly /mnt/hgfs. Can you try moving the installer to /var/tmp and installing from there? And could you please send me the output of this command: cat /etc/mtab thanks, Nat (* search terms: "operation not supported" tar)
Daqi Tu wrote:
Hi,
I was trying to install the 32 bit Phenix-dev-782 or the official release 1.7.1-743 onto a virtual ubuntu 10.04 32-bit machine. Both of them failed with this error:
/bin/tar: ./build/intel-linux-2.6/base/bin/wx-config: Cannot create symlink to `/net/longnose/scratch2/phenix/phenix-dev-782/build/intel-linux-2.6/base/lib/wx/config/gtk2-ansi-release-2.8':
Operation not supported /bin/tar: Exiting with failure status due to previous errors /mnt/hgfs/windubuntu/phenix-installer-dev-782/bin/install-from-binary: 352: /usr/local/phenix-dev-782/build/intel-linux-2.6/base/bin/python: not found
Any comments?
Yes, I've seen the the same error show up in var/log/messages after installing phenix (although it didn't interfere with the install): Sep 9 18:06:32 oswego automount[2319]: lookup_mount: exports lookup failed for longnose (about 67 times) Longnose is (or was) one of the serpentine clan of computers at LBL - so I suspected some directory exported by longnose was in a search-path of the phenix install. "grep" and "strings" located it to libtbx_refresh.pyc: strings build-binary/intel-linux-2.6/oswego/tmp/binary/solve_resolve/libtbx_refresh.pyc gives: /net/longnose/scratch2/phenix/phenix-1.6.4-486/solve_resolve/libtbx_refresh.pyt That was the fc3 32-bit version. Fedora12 64 bit gave no errors (but I think autofs was not running) and the specified files do not reference longnose. But that may be because longnose and co. have been retired and replaced by cage (one cage to bring them all, and in the darkness bind them?): strings phenix-installer-1.6.4-486/build-binary/*/erie/tmp/binary/solve_resolve/libtbx_refresh.pyc /net/cage/raid1/phenix/phenix-1.6.4-486/solve_resolve/libtbx_refresh.pyt <module> Maybe your virtual machine is more sensitive and shuts down the process when a referenced file doesn't exist. Or maybe it's just scared of snakes!
Thanks.
Daqi Tu _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Fri, Jun 10, 2011 at 6:15 PM, Edward A. Berry
Yes, I've seen the the same error show up in var/log/messages after installing phenix (although it didn't interfere with the install):
Sep 9 18:06:32 oswego automount[2319]: lookup_mount: exports lookup failed for longnose (about 67 times)
Longnose is (or was) one of the serpentine clan of computers at LBL - so I suspected some directory exported by longnose was in a search-path of the phenix install.
No, that's where we actually build it - Linux (unlike Macs) is quite happy to relocate libraries and has no problem loading them if LD_LIBRARY_PATH is set correctly. The installer will rewrite all of the paths required to actually run Phenix; what you're seeing is probably the effect of stray symlinks which we don't handle. As I said, this rarely breaks anything, but we did have one report recently of the GUI taking ~10 minutes to launch because the automounter wasn't timing out. So I may need to revisit the symlink issue. Of course, installing from source will always avoid these problems - but in most cases it is not worth the time and trouble. Fedora12 64 bit gave no errors (but I think autofs was not running) and the
specified files do not reference longnose. But that may be because longnose and co. have been retired and replaced by cage (one cage to bring them all, and in the darkness bind them?)
No, we're keeping longnose around as long as possible - the FC3 build is still the most compatible, even if it takes a while to finish. My guess is that all of the installers have the same problem, so if autofs was running I think you'd still see unexpected references to /net/cage. -Nat
participants (3)
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Daqi Tu -
Edward A. Berry -
Nathaniel Echols