; Best regards
> > Thierry
> >
> > -Original Message-
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Ed Pozharski
> > Sent: Monday, March 04, 2013 8:55 AM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] compilin
of bugs.
>
> Best regards
> Thierry
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
> Pozharski
> Sent: Monday, March 04, 2013 8:55 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] compiling refmac5 on Ub
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04
On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:
Running times were, correspondingly, 32.2s, 35.1s and 18.7s.
Numbers are almost too impressive to believe :)
How does it compare with ifort (which I thought should be the
On 03/04/2013 10:02 AM, Marcin Wojdyr wrote:
It also puzzled me, but I haven't done more careful benchmarking yet.
What did you get after compiling refmac?
My numbers are not as impressive, but I also get quite detectable
improvement, from 35s to 27s (ccp4-6.3.0 vs compiled from source). This
CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
Pozharski
Sent: Monday, March 04, 2013 8:55 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] compiling refmac5 on Ubuntu 12.04
On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:
> Running times were, correspondingly, 32.2s, 3
On 4 March 2013 13:55, wrote:
> On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:
>> Running times were, correspondingly, 32.2s, 35.1s and 18.7s.
>>
> Numbers are almost too impressive to believe :)
It also puzzled me, but I haven't done more careful benchmarking yet.
What did you get afte
On Mon, 2013-03-04 at 11:37 +, Marcin Wojdyr wrote:
> Running times were, correspondingly, 32.2s, 35.1s and 18.7s.
>
Numbers are almost too impressive to believe :)
How does it compare with ifort (which I thought should be the fastest
option on intel processors and thus unavailable (not free)
Indeed, the problem goes away when -static flag is omitted.
Interestingly, the resulting binary dependencies do not include any
ccp4-related libraries. For those interested, I was able to track the
segfault down to the close() operator - so basically it fails when
closing a file opened with ccpdpn
Adam,
On Mon, 2013-03-04 at 09:56 +, Adam Ralph wrote:
> One of the first routines called by CCP4
> progs is "ccp4fyp". This initialises the CCP4 environment.
I think you might have missed in my original post that I get an error
when I *do* source ccp4 environment.
>
> Does the error occur
Following what Marcin said, if you have a compiler other than gcc/gfortran
then I would definitely recommend compiling from source. Generally they
give much better performance and in addition there
might be optimised maths functions.
Adam
> One reason to compile refmac on Linux is that
One reason to compile refmac on Linux is that it can be faster.
I've just run $CEXAM/unix/runnable/refmac5-simple.exam example
with refmac from CCP4 6.3.0, from Garib's website and compiled with
GCC 4.7.2 only with -O3 option (all are 64-bit versions).
Running times were, correspondingly, 32.2s, 35
Dear all
I think this error has been dealt with (Ed will correct me if I am wrong). The
problem was -static in compilation. For whatever reason in some gcc (gfortran)
-static does not work (it compiles but has problems in running, what is the
reason is not clear to me). Sometimes in later gcc -
Dear Ed,
The error does indeed happen in ccp4lib. One of the first routines called by
CCP4
progs is "ccp4fyp". This initialises the CCP4 environment. See
lib/cctbx/cctbx_sources/ccp4io/lib/src/ccp4_general.c.
If you look at the code you can see that $CINCL is determined at run-time. You
ar
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Hello Ed,
did you try creating a ccp4 tree from source and replacing the refmac
source? Maybe that ccp4 environment will help you compile refmac - at
least with refmac I had the least trouble compiling when I got the
ccp4 source.
Why are you trying t
On Wed, Feb 27, 2013 at 12:27:46PM -0500, Ed Pozharski wrote:
> I am trying to compile refmac from source on a machine running Ubuntu
> 12.04. In a nutshell, after some troubleshooting I end up with
> executable that generates a segmentation fault. Log-file states that
>
> >> CCP4 library si
Adam,
I am not compiling CCP4, just refmac. IIUC, all that sourcing
ccp4.setup does is it sets $CLIB for refmac makefile to find libccp4c
and libccp4f. And presumably lapack and libblas, but that's a separate
issue.
On Thu, 2013-02-28 at 10:28 +, Adam Ralph wrote:
> Hi Ed,
>
>
>It loo
Hi Ed,
It looks as though you have not sourced $CCP4/include/ccp4.setup.
This needs to be customized and sourced before you configure and make
CCP4.
Adam
I am trying to compile refmac from source on a machine running Ubuntu
12.04. In a nutshell, after some troubleshooting I end up with
executable that generates a segmentation fault. Log-file states that
>> CCP4 library signal ccp4_parser:Failed to open external command
file (Success)
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