libEM/sparx/util_sparx.cpp does not compile on CentOS6 6.7 ? about eman2 HOT 6 CLOSED

Others have seen something similar recently. It appears to be a bad header in one of the CENTOS FFTW rpms. If you recompile and install FFTW from source this has solved the problem in at least 1 case.

Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol. Those who do
Co-Director National Center For Macromolecular Imaging ARE
Baylor College of Medicine The converse
[email protected] -or- [email protected] also applies
http://ncmi.bcm.edu/~stevel

On Aug 4, 2016, at 4:46 PM, buildqa [email protected] wrote:

I see the following error when trying to build with gcc on CentOS 6.7,

libEM/sparx/util_sparx.cpp:26532: error: ‘fftwf_alloc_real’ was not declared in this scope

.... and the source file lists,

26529 #ifdef _WIN32
26530         float cvv = (float *) malloc(2sizesizeof(float));
26531 #else
26532         float *cvv = fftwf_alloc_real(2size);
26533 #endif  //_WIN32
26534

There is no other instance of "fftwf_alloc_real" in this file. I'm building with libfftw3f.so.3.3.2. I have not built the source in a few months, but this configuration used to work.

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from eman2.

Hi

This is a valid fftw function. I would assume recompilation of fftw library would help.

Regards,
Pawel

On Aug 4, 2016, at 4:46 PM, buildqa [email protected] wrote:

I see the following error when trying to build with gcc on CentOS 6.7,

libEM/sparx/util_sparx.cpp:26532: error: ‘fftwf_alloc_real’ was not declared in this scope

.... and the source file lists,

26529 #ifdef _WIN32
26530         float cvv = (float *) malloc(2sizesizeof(float));
26531 #else
26532         float *cvv = fftwf_alloc_real(2size);
26533 #endif  //_WIN32
26534

There is no other instance of "fftwf_alloc_real" in this file. I'm building with libfftw3f.so.3.3.2. I have not built the source in a few months, but this configuration used to work.

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from eman2.

Hello and thanks for the follow-ups.

I saved the git log and went thru it, then after looking at

662 commit 47bb469
663 Author: Pawel [email protected]
664 Date: Mon Jul 18 17:44:53 2016 -0500
665
666 fftw in util
667
668 commit e551f49
669 Merge: b675ced 0ad35c2
670 Author: James Michael Bell [email protected]
671 Date: Mon Jul 18 16:22:29 2016 -0500
672
673 Merge branch 'master' of github.com:cryoem/eman2
674

.. I checked out using hash e551f49, and now everything builds again. I know this does not necessarily mean that the the very next commit broke compilation, but something after that did.

On my build system this is what I have for fftw libs,

$ cat /etc/redhat-release
CentOS release 6.7 (Final)

$ yum list installed | grep fftw
fftw.x86_64 3.2.1-3.1.el6 @base
fftw-devel.x86_64 3.2.1-3.1.el6 @base
fftw2.x86_64 2.1.5-21.el6 @epel
fftw2-devel.x86_64 2.1.5-21.el6 @epel

$ yum list available | grep fftw
fftw.i686 3.2.1-3.1.el6 base
fftw-devel.i686 3.2.1-3.1.el6 base
fftw-static.x86_64 3.2.1-3.1.el6 base
fftw2.i686 2.1.5-21.el6 epel
fftw2-devel.i686 2.1.5-21.el6 epel
fftw2-static.i686 2.1.5-21.el6 epel
fftw2-static.x86_64 2.1.5-21.el6 epel
root-fftw.x86_64 5.34.36-1.el6 epel

So it looks like I have the latest shared 64 bit devel and non-revel fftw and fftw2 libs installed, but now these do not work with the source code changes after ~7/18 because of the addition of some new fftw function? I don't see how uninstalling and re-installing the same RPM's is going to fix that. Are you folks adding a dependency on a different versions of fftw libs? I would be interested to know what version of these RPM's and/or the fftw libs you are building against.

Thanks again.

from eman2.

Hi

Fftw2 is the previous version of the library. We are using fftw3, version 3.3.4.

Regards,
Pawel

On Aug 5, 2016, at 3:17 AM, buildqa [email protected] wrote:

Hello and thanks for the follow-ups.

I saved the git log and went thru it, then after looking at

662 commit 47bb469
663 Author: Pawel [email protected]
664 Date: Mon Jul 18 17:44:53 2016 -0500
665
666 fftw in util
667
668 commit e551f49
669 Merge: b675ced 0ad35c2
670 Author: James Michael Bell [email protected]
671 Date: Mon Jul 18 16:22:29 2016 -0500
672
673 Merge branch 'master' of github.com:cryoem/eman2
674

.. I checked out using hash e551f49, and now everything builds again. I know this does not necessarily mean that the the very next commit broke compilation, but something after that did.

On my build system this is what I have for fftw libs,

$ cat /etc/redhat-release
CentOS release 6.7 (Final)

$ yum list installed | grep fftw
fftw.x86_64 3.2.1-3.1.el6 @base

fftw-devel.x86_64 3.2.1-3.1.el6 @base

fftw2.x86_64 2.1.5-21.el6 @epel

fftw2-devel.x86_64 2.1.5-21.el6 @epel

$ yum list available | grep fftw
fftw.i686 3.2.1-3.1.el6 base

fftw-devel.i686 3.2.1-3.1.el6 base

fftw-static.x86_64 3.2.1-3.1.el6 base

fftw2.i686 2.1.5-21.el6 epel

fftw2-devel.i686 2.1.5-21.el6 epel

fftw2-static.i686 2.1.5-21.el6 epel

fftw2-static.x86_64 2.1.5-21.el6 epel

root-fftw.x86_64 5.34.36-1.el6 epel

So it looks like I have the latest shared 64 bit devel and non-revel fftw and fftw2 libs installed, but now these do not work with the source code changes after ~7/18 because of the addition of some new fftw function? I don't see how uninstalling and re-installing the same RPM's is going to fix that. Are you folks adding a dependency on a different versions of fftw libs? I would be interested to know what version of these RPM's and/or the fftw libs you are building against.

Thanks again.

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from eman2.

Hi

Let me add one more thing. I did try to use yum and/or rocks in the past, but I found the experience frustrating. The reason was the same kind of problems you are experiencing. In short, it was difficult to figure what versions of libraries were installed and how to move around them. As soon as I switched to loading libraries directly from the developers life became easier.

Regards,
Pawel

On Aug 5, 2016, at 3:17 AM, buildqa [email protected] wrote:

Hello and thanks for the follow-ups.

I saved the git log and went thru it, then after looking at

662 commit 47bb469
663 Author: Pawel [email protected]
664 Date: Mon Jul 18 17:44:53 2016 -0500
665
666 fftw in util
667
668 commit e551f49
669 Merge: b675ced 0ad35c2
670 Author: James Michael Bell [email protected]
671 Date: Mon Jul 18 16:22:29 2016 -0500
672
673 Merge branch 'master' of github.com:cryoem/eman2
674

.. I checked out using hash e551f49, and now everything builds again. I know this does not necessarily mean that the the very next commit broke compilation, but something after that did.

On my build system this is what I have for fftw libs,

$ cat /etc/redhat-release
CentOS release 6.7 (Final)

$ yum list installed | grep fftw
fftw.x86_64 3.2.1-3.1.el6 @base

fftw-devel.x86_64 3.2.1-3.1.el6 @base

fftw2.x86_64 2.1.5-21.el6 @epel

fftw2-devel.x86_64 2.1.5-21.el6 @epel

$ yum list available | grep fftw
fftw.i686 3.2.1-3.1.el6 base

fftw-devel.i686 3.2.1-3.1.el6 base

fftw-static.x86_64 3.2.1-3.1.el6 base

fftw2.i686 2.1.5-21.el6 epel

fftw2-devel.i686 2.1.5-21.el6 epel

fftw2-static.i686 2.1.5-21.el6 epel

fftw2-static.x86_64 2.1.5-21.el6 epel

root-fftw.x86_64 5.34.36-1.el6 epel

So it looks like I have the latest shared 64 bit devel and non-revel fftw and fftw2 libs installed, but now these do not work with the source code changes after ~7/18 because of the addition of some new fftw function? I don't see how uninstalling and re-installing the same RPM's is going to fix that. Are you folks adding a dependency on a different versions of fftw libs? I would be interested to know what version of these RPM's and/or the fftw libs you are building against.

Thanks again.

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from eman2.

This issue is very old. Closing.

from eman2.