[gmx-users] patched version installation for free energy

[Justin Lemkul]

On 7/1/15 7:39 PM, Ahmet Yıldırım wrote:
> 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?
>

As I said, it's already merged.  You don't need to patch anything.

1. git clone git://git.gromacs.org/gromacs.git
2. Install the code
3. Profit?

-Justin

> 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.
>>
>
>
>

-- 
==================================================

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

==================================================