Sam Stampfer Samuel.Stampfer at tufts.edu
Tue Aug 25 13:13:44 PDT 2009

I couldn't get the source code to compile- the final message was: "error:
configuration step incomplete, exiting".  Any ideas?

[A copy of my problem is pasted here]:

I'm running the latest complete version of phenix (version 1.4-147, on Linux
2.6-x86 64).  When I run my .csh file I get the following error (with the 4
previous lines included):



  /lib64/libc.so.6 [0x30fca322a0]
Segmentation fault (Python and libc call stacks above)
                This crash may be due to a problem in any imported
                Python module, including modules which are not part
                of the cctbx project. To disable the traps leading
                to this message, define these environment variables
                (e.g. assign the value 1):
                This will NOT solve the problem, just mask it, but
                may allow you to proceed in case it is not critical.

When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run my
.csh file, it runs for a slightly longer period of time before ending with a
different error:

311240e000-3112410000 rw-p 0000e000 fd:00 14237822
2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0
2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0
2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0
2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0
2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920
2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920
2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920
2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941
2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941

However, the file ran fine and successfully output an improved .pdb file
without any BOOST-related problems on my PI's Mac- she is running version 95
of Phenix (which I was unable to obtain for linux- is it available

Can you help me with this?



On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve
<rwgk at cci.lbl.gov>wrote:

> Could you try with a source installation?
> https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show_source=1
> I recommend you rm -rf the binary installation before ./install from
> sources.
> Add
>  --nproc=N
> to the ./install command to use all N cpus in your machine for the
> installation.
> Let me know if the problem persists.
> Ralf
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090825/78dda0f9/attachment-0003.htm>

More information about the phenixbb mailing list