*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi Charles,
ldd /bin/mkdir
libc.so.6 => /lib/libc.so.6 (0x00002aaaaabc2000)
/lib64/ld-linux-x86-64.so.2 (0x00002aaaaaaab000)
as I said,
/lib/libc.so.6 -> libc-2.3.5.so
The permissions of libc-2.3.5.so are (-rw-r--r--)
The other one is also a link:
/lib64/ld-linux-x86-64.so.2 -> ld-2.3.5.so
and ld-2.3.5.so has permissions (-rwxr-xr-x)
Still puzzled...
Miguel
Charles Ballard wrote:
> 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:
>
>> *** For details on how to be removed from this list visit the ***
>> *** CCP4 home page http://www.ccp4.ac.uk ***
>>
>>
> 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:
>>>>>>>>>>
>>>>>>>>>>> *** For details on how to be removed from this list visit
>>>>>>>>>>> the ***
>>>>>>>>>>> *** CCP4 home page http://www.ccp4.ac.uk ***
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>> 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]
>>>>>>> -
>>>>>>> ------------------------------------------------------------------- -
>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>
>
>
> --
> 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]
> - ----------------------------------------------------------------------
> 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
>>
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.1 (GNU/Linux)
iD8DBQFEDWuQF6oOrDvhbQIRAvDIAKCbmYg1Oh2sCfAfDIfQ1j8biUrNMQCfR5VY
YLi9dDQJieQ9ABQ+SauZtpE=
=sehO
-----END PGP SIGNATURE-----
