Missing, not found Eigen3 during VOTCA installation

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Andrey Brukhno

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Jul 18, 2018, 2:04:00 PM7/18/18
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Hello,

The last time I was installing the CSG package in my Ubuntu (up-to-date 2014 LTS) I got this error from cmake: eigen3 not found, with a suggestion to provide the path to it. I then downloaded the library from their website, installed it and added its include directory to both my $PATH and to the environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake still complained and stopped with the same error, even when I fed it the flag: -DEIGEN3_INCLUDE_DIR=<destination>.

Not sure what went wrong, but I had to use alternative way of installation via spack, and it worked eventually, although it lloked like spack installed ALL the dependencies along with VOTCA in a separate directory, which is of course an overkill.

I suppose this post is just to notify the current developers that there might be some issue with finding an exiasting Eigen3 dir.

Thanks
Andrey

Christoph Junghans

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Jul 18, 2018, 2:20:47 PM7/18/18
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On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca
<vo...@googlegroups.com> wrote:
> Hello,
>
> The last time I was installing the CSG package in my Ubuntu (up-to-date 2014
> LTS) I got this error from cmake: eigen3 not found, with a suggestion to
> provide the path to it. I then downloaded the library from their website,
> installed it and added its include directory to both my $PATH and to the
> environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake still
> complained and stopped with the same error, even when I fed it the flag:
> -DEIGEN3_INCLUDE_DIR=<destination>.
Just a reminder that 2014 was already 4 years ago ;-)
We recently fixed an issue in the Eigen3 detection:
https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
which includes:
https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf
Did you use that version?

>
> Not sure what went wrong, but I had to use alternative way of installation
> via spack, and it worked eventually, although it lloked like spack installed
> ALL the dependencies along with VOTCA in a separate directory, which is of
> course an overkill.
That is Spack's design, so don't complain to me! And yes we need to
update the dependencies of the VOTCA package in Spack.
>
> I suppose this post is just to notify the current developers that there
> might be some issue with finding an exiasting Eigen3 dir.
Thanks for letting us know, can you try if above versions fix the issue for you?

Christoph
>
> Thanks
> Andrey
>
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Christoph Junghans

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Jul 19, 2018, 10:27:52 AM7/19/18
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On Wed, Jul 18, 2018 at 12:20 PM, Christoph Junghans <jung...@votca.org> wrote:
> On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca
> <vo...@googlegroups.com> wrote:
>> Hello,
>>
>> The last time I was installing the CSG package in my Ubuntu (up-to-date 2014
>> LTS) I got this error from cmake: eigen3 not found, with a suggestion to
>> provide the path to it. I then downloaded the library from their website,
>> installed it and added its include directory to both my $PATH and to the
>> environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake still
>> complained and stopped with the same error, even when I fed it the flag:
>> -DEIGEN3_INCLUDE_DIR=<destination>.
> Just a reminder that 2014 was already 4 years ago ;-)
> We recently fixed an issue in the Eigen3 detection:
> https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
> which includes:
> https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
> https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf
> Did you use that version?
>
>>
>> Not sure what went wrong, but I had to use alternative way of installation
>> via spack, and it worked eventually, although it lloked like spack installed
>> ALL the dependencies along with VOTCA in a separate directory, which is of
>> course an overkill.
> That is Spack's design, so don't complain to me! And yes we need to
> update the dependencies of the VOTCA package in Spack.
https://github.com/spack/spack/pull/8757

Andrey Brukhno

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Jul 19, 2018, 11:33:18 AM7/19/18
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On Thursday, July 19, 2018 at 3:27:52 PM UTC+1, Christoph Junghans wrote:
On Wed, Jul 18, 2018 at 12:20 PM, Christoph Junghans <jung...@votca.org> wrote:
> On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca
> <vo...@googlegroups.com> wrote:
>> Hello,
>>
>> The last time I was installing the CSG package in my Ubuntu (up-to-date 2014
>> LTS) I got this error from cmake: eigen3 not found, with a suggestion to
>> provide the path to it. I then downloaded the library from their website,
>> installed it and added its include directory to both my $PATH and to the
>> environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake still
>> complained and stopped with the same error, even when I fed it the flag:
>> -DEIGEN3_INCLUDE_DIR=<destination>.
> Just a reminder that 2014 was already 4 years ago ;-)

Thanks, up to now it did not hurt to stay with that version, but eventually yes an upgrade is pending. :)
No, I have not tried any newer version yet. My aim was to get the latest release installed, which spack did succeed to do (v1.4.1).

BTW, when I tried to install with apt-get nothing happened: no votca package found. Perhaps it would only work for 2016(+) Ubuntu?
 
>
>>
>> Not sure what went wrong, but I had to use alternative way of installation
>> via spack, and it worked eventually, although it lloked like spack installed
>> ALL the dependencies along with VOTCA in a separate directory, which is of
>> course an overkill.
> That is Spack's design, so don't complain to me! And yes we need to
> update the dependencies of the VOTCA package in Spack.
https://github.com/spack/spack/pull/8757

I see... Otherwise I also noticed that spack installs csg and tools separately in two directories beside each other. But then VOTCARC.bash etc occur in the tools/bin and VOTCASHARE points at votca_tools/share instead of votca_csg/share, so the scripts/inverse are not found. I had to reset VOTCASHARE correctly in my .bashrc. 

I mentioned this for other users to be aware.
 
Andrey

Christoph Junghans

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Jul 19, 2018, 11:48:14 AM7/19/18
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On Thu, Jul 19, 2018 at 9:33 AM, 'Andrey Brukhno' via votca
But then I don't understand your original error because votca-csg
1.4.1 doesn't depend on Eigen3.

>
> BTW, when I tried to install with apt-get nothing happened: no votca package
> found. Perhaps it would only work for 2016(+) Ubuntu?
Yes, only 2016.4 and later:
https://packages.ubuntu.com/search?keywords=votca-csg&searchon=names&suite=all&section=all
and v1.4.1 only in Ubuntu 18.04!

>
>>
>> >
>> >>
>> >> Not sure what went wrong, but I had to use alternative way of
>> >> installation
>> >> via spack, and it worked eventually, although it lloked like spack
>> >> installed
>> >> ALL the dependencies along with VOTCA in a separate directory, which is
>> >> of
>> >> course an overkill.
>> > That is Spack's design, so don't complain to me! And yes we need to
>> > update the dependencies of the VOTCA package in Spack.
>> https://github.com/spack/spack/pull/8757
>
>
> I see... Otherwise I also noticed that spack installs csg and tools
> separately in two directories beside each other. But then VOTCARC.bash etc
> occur in the tools/bin and VOTCASHARE points at votca_tools/share instead of
> votca_csg/share, so the scripts/inverse are not found. I had to reset
> VOTCASHARE correctly in my .bashrc.
Good point I will have to think, how to fix that. I think the VOTCARC
file should get installed to start with as csg_inverse will
auto-detect the location (using csg_call in your PATH) if VOTCASHARE
isn't set.

Christoph

Andrey Brukhno

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Jul 19, 2018, 12:57:23 PM7/19/18
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On Thursday, July 19, 2018 at 4:48:14 PM UTC+1, Christoph Junghans wrote:
>>
>> > We recently fixed an issue in the Eigen3 detection:
>> >
>> > https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
>> > which includes:
>> >
>> > https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
>> >
>> > https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf
>> > Did you use that version?
>
>
> No, I have not tried any newer version yet. My aim was to get the latest
> release installed, which spack did succeed to do (v1.4.1).
But then I don't understand your original error because votca-csg
1.4.1 doesn't depend on Eigen3.

I guess I meant (implicitly) that I tried to follow the instructions for installation using cmake found on one of the VOTCA's webpages, and that's when I encountered the error message about eigen3 (not sure now what version it was, but I think 1.5.1). But then I went the spack way and was satisfied. Since then I have not tried cmake for any other version. But I may try on my home PC soon.

Christoph Junghans

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Jul 19, 2018, 3:19:03 PM7/19/18
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On Thu, Jul 19, 2018 at 10:57 AM, 'Andrey Brukhno' via votca
<vo...@googlegroups.com> wrote:
>
>
> On Thursday, July 19, 2018 at 4:48:14 PM UTC+1, Christoph Junghans wrote:
>>
>> >>
>> >> > We recently fixed an issue in the Eigen3 detection:
>> >> >
>> >> >
>> >> > https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
>> >> > which includes:
>> >> >
>> >> >
>> >> > https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
>> >> >
>> >> >
>> >> > https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf
>> >> > Did you use that version?
>> >
>> >
>> > No, I have not tried any newer version yet. My aim was to get the latest
>> > release installed, which spack did succeed to do (v1.4.1).
>> But then I don't understand your original error because votca-csg
>> 1.4.1 doesn't depend on Eigen3.
>
>
> I guess I meant (implicitly) that I tried to follow the instructions for
> installation using cmake found on one of the VOTCA's webpages, and that's
> when I encountered the error message about eigen3 (not sure now what version
> it was, but I think 1.5.1). But then I went the spack way and was satisfied.
> Since then I have not tried cmake for any other version. But I may try on my
> home PC soon.
I see, it is a bit confusing in the README of the new buildsystem,
hopefully that makes it more clear:
https://github.com/votca/votca/commit/40cbeb2daf4b4647292cf423e9755125cb7c3380

Christoph

Andrey Brukhno

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Jul 19, 2018, 6:49:54 PM7/19/18
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Ok, I will give it a try on my home PC.

Andrey

Andrey Brukhno

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Jul 20, 2018, 1:08:31 PM7/20/18
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Christoph,

What is the flag for cmake not to search for SQLITE3?

Thanks
Andrey



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Christoph Junghans

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Jul 20, 2018, 4:56:21 PM7/20/18
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On Fri, Jul 20, 2018 at 11:08 AM, 'Andrey Brukhno' via votca
<vo...@googlegroups.com> wrote:
> Christoph,
>
> What is the flag for cmake not to search for SQLITE3?
WITH_SQLITE3=OFF, btw you can just look up the options in ccmake.

Christoph
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Andrey Brukhno

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Jul 20, 2018, 5:12:01 PM7/20/18
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The problem is, I remembered this option for the old build script and tried to use it with cmake but still got the error "sqlite3 not found".

Andrey

Christoph Junghans

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Jul 20, 2018, 5:41:00 PM7/20/18
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On Fri, Jul 20, 2018 at 3:11 PM, 'Andrey Brukhno' via votca
<vo...@googlegroups.com> wrote:
> The problem is, I remembered this option for the old build script and tried
> to use it with cmake but still got the error "sqlite3 not found".
Which version of VOTCA are you using now?

Andrey Brukhno

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Jul 20, 2018, 6:49:32 PM7/20/18
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Well, I tried to follow your instructions in this thread for "stable" branch.

Andrey

Christoph Junghans

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Jul 20, 2018, 8:49:10 PM7/20/18
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On Fri, Jul 20, 2018, 16:49 'Andrey Brukhno' via votca <vo...@googlegroups.com> wrote:
Well, I tried to follow your instructions in this thread for "stable" branch.
Just checked, worked for me. Can you open an github issue with all the details (commands, output etc.)

Thanks,

Christoph

Andrey


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Andrey Brukhno

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Jul 20, 2018, 8:59:00 PM7/20/18
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By now I have installed SQLITE3, compiled latest version of Gromacs and currently installing VOTCA.
BTW, the Gromacs flag  -DWITH_GMX=ON did not work for me either.
Not sure what was the issue with the flag -DWITH_SQLITE3=OFF, but my cmake version was below 3, so I had to reinstall it too.

Thanks
Andrey

Christoph Junghans

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Jul 21, 2018, 2:33:16 PM7/21/18
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I dropped the install of the confusing VOTCARC in:
Christoph 

Christoph Junghans

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On Fri, Jul 20, 2018 at 18:59 'Andrey Brukhno' via votca <vo...@googlegroups.com> wrote:
By now I have installed SQLITE3, compiled latest version of Gromacs and currently installing VOTCA.

BTW, the Gromacs flag  -DWITH_GMX=ON did not work for me either.
Can you be a bit more specific what the problem was?


Not sure what was the issue with the flag -DWITH_SQLITE3=OFF, but my cmake version was below 3, so I had to reinstall it too.
Yeah, due to using C++11 we need CMake-3.1 now, but that should give an error immediately.

Christoph 

Thanks
Andrey




Andrey

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Andrey Brukhno

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Jul 21, 2018, 10:26:06 PM7/21/18
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Ok, good to know! - Not that I could follow the workflow by the link though.

Andrey



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Andrey Brukhno

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Jul 21, 2018, 10:36:49 PM7/21/18
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On Sat, Jul 21, 2018 at 7:42 PM, Christoph Junghans <jung...@votca.org> wrote:


On Fri, Jul 20, 2018 at 18:59 'Andrey Brukhno' via votca <vo...@googlegroups.com> wrote:
By now I have installed SQLITE3, compiled latest version of Gromacs and currently installing VOTCA.
I think i found that issue and fixed it in:

Good to know!

+if(DEFINED WITH_SQLITE3 AND NOT WITH_SQLITE3)

sounds weird - perhaps it's just the computer logic :) just kidding...
 

BTW, the Gromacs flag  -DWITH_GMX=ON did not work for me either.
Can you be a bit more specific what the problem was?


I wanted VOTCA to install Gromacs along with itself as it did before (build script for v1.3 did),
but the flag -DWITHGMX=ON provided to cmake did not do that (seemed like it ignored the flag), 
so I had to install Gromacs newest version by myself.
 

Not sure what was the issue with the flag -DWITH_SQLITE3=OFF, but my cmake version was below 3, so I had to reinstall it too.
Yeah, due to using C++11 we need CMake-3.1 now, but that should give an error immediately.


Yes, I was installing on my laptop and did not check the cmake version first.
Then, after checking it, I was surprised it did not complain as it did on my work desktop.

Andrey
 
Christoph 

Thanks
Andrey




Andrey


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>> Christoph Junghans
>> Web: http://www.compphys.de
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>
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--
Christoph Junghans
Web: http://www.compphys.de

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You received this message because you are subscribed to a topic in the Google Groups "votca" group.
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To post to this group, send email to vo...@googlegroups.com.
Visit this group at https://groups.google.com/group/votca.
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You received this message because you are subscribed to the Google Groups "votca" group.
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To post to this group, send email to vo...@googlegroups.com.
Visit this group at https://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.
--
Christoph Junghans
Web: http://www.compphys.de

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