[gmx-users] patched version installation for free energy

[Ahmet Yıldırım]

Thanks. I think this command "git clone git://git.gromacs.org/gromacs.git
pulls the latest version"? But I need the patched version. How can I pull
the patched version (
https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c)
via git?

2015-07-02 1:02 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 7/1/15 7:00 PM, Ahmet Yıldırım wrote:
>
>> Hi Justin,
>>
>> Do you think that there is a bug? If yes, what will we do now?
>>
>>
> Doubtful.  I installed that code myself to test it.  Of course, I got it
> directly from the GROMACS repository via Gerrit, but I doubt that makes a
> difference.  I can't explain your observation; the code should install
> cleanly if done correctly.  Maybe someone else has an idea.
>
> FWIW, the latest master and release-5-1 branches have the intermolecular
> bondeds code, so you could try pulling either via git and installing that
> version.
>
> -Justin
>
>
>  2015-07-01 19:09 GMT+02:00 Ahmet Yıldırım <ahmedo047 at gmail.com>:
>>
>>  :) yes.
>>>
>>> 2015-07-01 19:08 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>>>
>>>
>>>>
>>>> On 7/1/15 1:05 PM, Ahmet Yıldırım wrote:
>>>>
>>>>  I am already trying to install it into a separate directory. Source
>>>>> files
>>>>> is in the gromacs-patched folder. I created "gromacs" directory away
>>>>> from
>>>>> $HOME/Public/gromacs-patched.
>>>>>
>>>>>
>>>>>  And you get the same error, even after starting from a fresh build
>>>> directory?
>>>>
>>>> -Justin
>>>>
>>>>
>>>>   2015-07-01 18:56 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On 7/1/15 12:52 PM, Ahmet Yıldırım wrote:
>>>>>>
>>>>>>   Hi,
>>>>>>
>>>>>>>
>>>>>>> When I install the patched GROMACS version (
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> https://github.com/gromacs/gromacs/tree/022ad08b2fd0c1de085e88ac81a61841c4daea9c
>>>>>>> )
>>>>>>> on cluster, I get the following error after command-2. Why do I get
>>>>>>> this
>>>>>>> error?
>>>>>>>
>>>>>>> Command-1:
>>>>>>> t-mn01 [~/Public/gromacs]$ cmake ../gromacs-patched -DGMX_GPU=OFF
>>>>>>> -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/a/user/Public/gromacs
>>>>>>>
>>>>>>>
>>>>>>>   Don't install into the source tree.
>>>>>>>
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>    ....
>>>>>>
>>>>>>  -- Configuring done
>>>>>>> -- Generating done
>>>>>>> -- Build files have been written to: /home/a/user/Public/gromacs
>>>>>>>
>>>>>>> Command-2:
>>>>>>> t-mn01 [~/Public/gromacs]$ make -j 8 install
>>>>>>>
>>>>>>> ....
>>>>>>> -- Installing:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> /home/a/user/Public/gromacs/include/gromacs/trajectoryanalysis/cmdlinerunner.h
>>>>>>> CMake Error at src/programs/cmake_install.cmake:42 (FILE):
>>>>>>>      file INSTALL cannot find
>>>>>>> "/home/a/user/Public/gromacs/bin/gmx_mpi".
>>>>>>> Call Stack (most recent call first):
>>>>>>>      src/cmake_install.cmake:40 (INCLUDE)
>>>>>>>      cmake_install.cmake:44 (INCLUDE)
>>>>>>>
>>>>>>>
>>>>>>> make: *** [install] Error 1
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>   --
>>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> Justin A. Lemkul, Ph.D.
>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>
>>>>>> Department of Pharmaceutical Sciences
>>>>>> School of Pharmacy
>>>>>> Health Sciences Facility II, Room 629
>>>>>> University of Maryland, Baltimore
>>>>>> 20 Penn St.
>>>>>> Baltimore, MD 21201
>>>>>>
>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>> posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 629
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>>
>>> --
>>> Ahmet Yıldırım
>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Ahmet Yıldırım