[gmx-users] Version problem
Johnny Lu
johnny.lu128 at gmail.com
Thu Nov 6 23:04:16 CET 2014
I typed an extra space that shouldn't be there.
$ find / -name mdrun* > mdrun_search
On Thu, Nov 6, 2014 at 5:03 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> can look for all files with name mdrun by
>
> $ find / -name mdrun * > mdrun_search
> and then
> $ cat mdrun_search
>
>
> On Thu, Nov 6, 2014 at 7:25 AM, Erik Marklund <erik.marklund at chem.ox.ac.uk
> > wrote:
>
>> Hi,
>>
>> 'which mdrun' only tells you the location of the mdrun you're currently
>> using and is no good here. How did you install 5.0.2? The CMake files
>> should tell you where installation directory is.
>>
>> Kind regards,
>> Erik
>>
>> On 6 Nov 2014, at 11:43, satya at physics.iisc.ernet.in wrote:
>>
>> >
>> > tried "which mdrun"
>> > showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded
>> > v5.0.2.tar.gz and used for installation.
>> >
>> >
>> >> try to find mdrun program by typing this command on terminal:
>> >> "which mdrun"
>> >> will show path of mdrun program where it located.
>> >> On Nov 6, 2014 4:01 PM, <satya at physics.iisc.ernet.in> wrote:
>> >>
>> >>> Dear Dr. Carsten Kutzner,
>> >>> I am unable to find the "gmx5/bin/GMXRC" in my machine,
>> >>> used 'locate' and 'find' to search the location.
>> >>> However I have source the following:
>> >>> source /usr/share/gromacs/shell-specific/GMXRC.bashrc
>> >>> Without this also mdrun is running. I am definitely missing something.
>> >>> Kindly help.
>> >>>
>> >>> With best regards,
>> >>>
>> >>> Satya
>> >>>
>> >>>> On 06 Nov 2014, at 07:15, satya at physics.iisc.ernet.in wrote:
>> >>>>
>> >>>>> Dear all,
>> >>>>> I am new to GROMACS, just finish installation of v5.0.2, started
>> >>> reading
>> >>>>> online manual, as instructed executed the command: mdrun -version
>> and
>> >>>>> the
>> >>>>> printout pasted below.
>> >>>>>
>> >>>>> It is printing GROMACS version 4.6.5, however I have installed
>> >>> version
>> >>>>> 5.0.2. What is the problem?
>> >>>> Find the directory to where you have installed your GROMACS 5.0
>> >>>> executables
>> >>>> and then do
>> >>>>
>> >>>> source /path/to/gmx5/bin/GMXRC
>> >>>>
>> >>>> which mdrun
>> >>>>
>> >>>> should now give you the 5.0 mdrun
>> >>>>
>> >>>> Carsten
>> >>>>
>> >>>>>
>> >>>>> Regards,
>> >>>>> Satyabrata Das
>> >>>>>
>> >>>>>
>> ======================================================================
>> >>>>> Program: mdrun
>> >>>>> Gromacs version: VERSION 4.6.5
>> >>>>> Precision: single
>> >>>>> Memory model: 64 bit
>> >>>>> MPI library: thread_mpi
>> >>>>> OpenMP support: enabled
>> >>>>> GPU support: disabled
>> >>>>> invsqrt routine: gmx_software_invsqrt(x)
>> >>>>> CPU acceleration: SSE4.1
>> >>>>> FFT library: fftw-3.3.3-sse2-avx
>> >>>>> Large file support: enabled
>> >>>>> RDTSCP usage: enabled
>> >>>>> Built on: Sun Dec 15 04:01:11 UTC 2013
>> >>>>> Built by: buildd at panlong [CMAKE]
>> >>>>> Build OS/arch: Linux 3.2.0-37-generic x86_64
>> >>>>> Build CPU vendor: GenuineIntel
>> >>>>> Build CPU brand: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz
>> >>>>> Build CPU family: 6 Model: 44 Stepping: 2
>> >>>>> Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
>> >>>>> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3
>> >>>>> sse4.1
>> >>>>> sse4.2 ssse3
>> >>>>> C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real
>> >>>>> (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2
>> >>>>> C compiler flags: -msse4.1 -Wextra
>> >>> -Wno-missing-field-initializers
>> >>>>> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
>> >>> -Wno-unused-parameter
>> >>>>> -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
>> >>>>> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3
>> >>>>> -DNDEBUG
>> >>>>> satyabrata at satyabrata-desktop:~$
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> --
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>> >>>>
>> >>>>
>> >>>> --
>> >>>> Dr. Carsten Kutzner
>> >>>> Max Planck Institute for Biophysical Chemistry
>> >>>> Theoretical and Computational Biophysics
>> >>>> Am Fassberg 11, 37077 Goettingen, Germany
>> >>>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> >>>> http://www.mpibpc.mpg.de/grubmueller/kutzner
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>> >>>>
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