[gmx-users] patched version installation for free energy

[Ahmet Yıldırım]

Hi Justin,

Do you think that there is a bug? If yes, what will we do now?

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
>>>>
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>>>>
>>>
>>>
>>>
>>>
>>>
>> --
>> ==================================================
>>
>> 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
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> Ahmet Yıldırım
>



-- 
Ahmet Yıldırım