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Hi Miguel,
That sounds OK as far as it goes. Can you do a ldd on mkdir
ldd mkdir
our RH FC2 system gives
libselinux.so.1 => /lib/libselinux.so.1 (0x009ef000)
libc.so.6 => /lib/tls/libc.so.6 (0x00baf000)
/lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x00b96000)
So, the first location of the libc.so.6 load is in /lib/tls . This is
then just
a softlink to /lib/tls/libc-2.3.3.so as in /lib (although the files are
different).
Charles
On Monday, March 6, 2006, at 09:09 PM, Miguel Ortiz-Lombardia wrote:
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Dear Charles and ccp4bb,
The first problem is that even that directory is not created. From the
make.log file:
making directory:
/usr/local/ccp4-6.0/src/phaser/phaser-1.3.2
mkdir: error while loading shared libraries: libc.so.6: cannot open
shared object file: No such file or directory
Then, other shell (and not) programs (such as touch, grep, awk, cp)
fail
with the same error about libc.so.6 missing. However, I do have this
library as a soft link:
/lib/libc.so.6 -> libc-2.3.5.so
One reason I have answered so late is that I tried to convert this in a
hard link, which broke my system: any command at the shell prompted the
same error about libc.so.6 and it became impossible to recover the
system. Thus, I had to re-install everything. I'm quite puzzle about
this problem.
I re-compiled everything as stated in my previous e-mail (Phaser failed
again, of course) and then noticed that some x-windows programs still
use gfortran even if I set up FC=g77 and F77=g77. These are the
programs
in the XCCPJIFFY directory. The compile fine with gfortran (4.0) and
they do work as expected on a few files I tried.
Also, this time I compiled using Tcl/Tk/Blt from Ubuntu. Just in case,
I
made a link to point 'bltwish' to 'wish'. I haven't found any problems
so far with ccp4i.
I ran all the tests (run-all in $CCP4/examples/unix/runnable) and got
no other error messages than the expected:
*** phaser.exam: phaser not found in CBIN
I'd appreciate any ideas on how to have phaser compiled.
Thank you for your help so far.
Cheers,
Miguel
Charles Ballard wrote:
Hi Miguel,
under $CCP4/src/phaser/build-final (under several layers giving os and
machine id) are the build logs
for phaser/cctbx. Can you send them to [EMAIL PROTECTED], and we will
take
a look.
Charles Ballard
CCP4
On Monday, March 6, 2006, at 10:06 AM, Miguel Ortiz Lombardia wrote:
Dear Charles,
As I said in a post that made just a few minutes after receiving your
e-email, I managed to compile everything (but Phaser). I have now
tested
mosflm and works wonderfully, at least up to the refinement of the
cell.
I have compiled everything as 64 bit.
Cheers,
Miguel
Charles Ballard wrote:
Dear Miguel,
we regularly build the suite on a RH Enterprise AMD machine (as 64
bit). The major sticking points are the bltwish and the X11.
Last time
I checked blt required some patching to get it to work as a 64 bit
application. The problem with our X libraries is that we only
have the
32 bit libraries, so no 64 bit
applications will compile against them :-). Your vendor supplied
lapack is probably 64 bit, as would be any fftw.
If you take the 32 bit route, you will either have to ensure that
your
compiler defaults to 32 bit, or force it to using -m32 (look at the
linux64 option in the ccp4 configure, it uses -m64).
Charles Ballard
CCP4
On Monday, March 6, 2006, at 02:45 AM, William Scott wrote:
Dear Tim:
Last time I tried to configure without /usr/bin/bltwish present,
the
configure for ccp4i failed. But I think "last time" was 5.0.2.
In any case, I made a Debian package that contains only the
missing
/usr/bin/bltwish (for i386/i686) should anyone want it.
http://xanana.ucsc.edu/linux/
All the best,
Bill
On Sun, 5 Mar 2006, Tim Gruene wrote:
Bill,
You do not need to build bltwish on Debian. You can install the
blt-library and replace any appearance of bltwish with wish. As
far
as I
remember that is two files, in particular $CCP4/ccp4i/bin/ccp4i.
Miguel:
Could you redirect the output from make to a log file and
post the error message, e.g. for mosflm?
It may help to also set F77=g77 when running the configure
script,
since
some configure scripts look for that variable rather than FC.
fftw
does
for example.
Cheers,
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Sun, 5 Mar 2006, William Scott wrote:
Hi Miguel:
I built CCP4 with ubunto on i386/i686 so I don't know how to
advise, but I
found that I needed to let ccp4 build its own fftw. Also I had
to
install
bltwish, as blt that comes with ubuntu (and all Debian linuxes)
apparently
lacks this one file. I don't know if any of that is relevant to
what you
are experiencing.
Bill
On Sun, 5 Mar 2006, Miguel Ortiz-Lombardia wrote:
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Dear all,
Has anyone succeded at make a complete build of CCP4 in a AMD64
system
under Ubuntu?
As advised for i386 using:
gcc=4.0
FC=g77 (3.4)
./configure --with-shared-libs --with-x --with-fftw=/usr linux
I can compile most of the programs, but some fail, notably phaser
and
many X-windows programs, including mosflm.
Thank you in advance for your help.
Cheers,
Miguel
--
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
-
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-
- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
-
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Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
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