When you see a file name like ~/.bashrc, the ~/ part says 'under my home
directory '.
So if you were to
$ vi ~/.bashrc
then you could add to that script. By the way, the . in .bashrc means
the file will not be seen by ls unless the -a argument is used or the
file name is given.
Bill
On 1/20/17 11:28 PM, Karla Galdamez wrote:
> Hi Hai,
>
> Thank you very much for this! It all configured well utilizing the
> command: ./configure -macAccelerate clang
>
> Subsequently, I followed the instructions recommended on the output screen
> (copied below).
> I, however, copied the commands below on the screen and did not 'add' to
> startup file ( e.g. ~/.bashrc) because I do not know where the file has
> been placed. Would you be able to tell me where I can go to modify start
> up file? - Thank You!
>
>
> --------------------------------------------------------------------
> Environment resource files are provided to set the proper environment
> variables to use AMBER and AmberTools. This is required to run any Python
> programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
>
> If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
> /Users/karlagaldamez/amber16/amber.sh file in your shell. Consider adding
> the line
> test -f /Users/karlagaldamez/amber16/amber.sh && source
> /Users/karlagaldamez/amber16/amber.sh
> to your startup file (e.g., ~/.bashrc)
>
> If you use a C shell (e.g., csh, tcsh), source the
> /Users/karlagaldamez/amber16/amber.csh file in your shell. Consider adding
> the line
> test -f /Users/karlagaldamez/amber16/amber.csh && source
> /Users/karlagaldamez/amber16/amber.csh
> to your startup file (e.g., ~/.cshrc)
>
> (You need to do the above before running 'make install')
>
> On Fri, Jan 20, 2017 at 9:58 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> can you try to follow the instruction here for MacOS?
>> http://ambermd.org/amber_install.html
>>
>> Basically:
>> ./configure -macAccelerate clang
>>
>> PS: IMO, Apply guys make "clang" sounds like GNU compiler.
>>
>> Hai
>>
>>
>> On Sat, Jan 21, 2017 at 12:53 AM, Karla Galdamez <kgalda.berkeley.edu>
>> wrote:
>>
>>> Hi everyone,
>>>
>>> Thank you for your previous response on installing AmberTools. I have
>>> followed the download on web link you mentioned below.
>>> http://ambermd.org/AmberTools16-get.html
>>> Then, I began to follow instructions on installment on pg.23 of Amber
>> 2016
>>> Reference manual under Sect. 2 Installation.
>>>
>>> I have executed the command (4):
>>>> ./configure --help
>>>> ./configure gnu
>>> And it looks like everything works well up to lgfortran. I am copying
>>> below the error listed. Would you have recommendations as to what to do
>>> next? - do you have a recommendation as to where to download lgfortran
>>> libraries for Mac OS? - Thank You!
>>>
>>> Testing the g++ compiler:
>>> g++ -fPIC -o testp testp.cpp
>>> OK
>>>
>>> Testing the gfortran compiler:
>>> gfortran -fPIC -O0 -o testp testp.f
>>> OK
>>>
>>> Testing mixed C/Fortran compilation:
>>> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o
>> testp.c.o
>>> testp.c
>>> gfortran -fPIC -O0 -c -o testp.f.o testp.f
>>> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
>>> testp.c.o testp.f.o -lgfortran -w
>>> ld: library not found for -lgfortran
>>> clang: error: linker command failed with exit code 1 (use -v to see
>>> invocation)
>>> ./configure2: line 2348: ./testp: No such file or directory
>>> Error: Unable to compile mixed C/Fortran code.
>>> Please check your compiler settings and configure flags.
>>> Configure failed due to the errors above!
>>>
>>> On Tue, Jan 17, 2017 at 10:47 PM, Nhai <nhai.qn.gmail.com> wrote:
>>>
>>>> Ah good point
>>>>
>>>> That link is meant to install required software to prepare for
>> installing
>>>> amber.
>>>>
>>>> You still need to download anbertools
>>>>
>>>> http://ambermd.org/AmberTools16-get.html
>>>>
>>>> Hai Nguyen
>>>>
>>>>> On Jan 18, 2017, at 1:24 AM, Karla Galdamez <kgalda.berkeley.edu>
>>> wrote:
>>>>> Hi,
>>>>>
>>>>> Thank you very much in advance for your help. I am trying to
>> download
>>>>> Amber on Mac OS from the link below.
>>>>> http://ambermd.org/amber_install.html
>>>>>
>>>>> I have followed the instructions including XCode, and typing the
>>>> suggested
>>>>> commands on the terminal line following instructions as suggested.
>>>>>
>>>>>
>>>>> Subsequently, I installed XQuartz, and gfortran. However, when I
>> write
>>>>> down the last command to install Amber: ./configure -macAccelerate
>>> clang,
>>>>> I obtain the response of : ' No such file or directory.
>>>>> I have included the command lines below.
>>>>>
>>>>> Thank you once more for your help!
>>>>> With kind regards,
>>>>> Karla
>>>>>
>>>>>
>>>>>> karlas-MacBook-Pro:~ karlagaldamez$ sudo xcodebuild -license
>>>>> Password:
>>>>> Apple Inc.
>>>>>
>>>>> Xcode and Apple SDKs Agreement
>>>>>
>>>>>
>>>>>> karlas-MacBook-Pro:~ karlagaldamez$ xcode-select --install
>>>>> xcode-select: error: command line tools are already installed, use
>>>>> "Software Update" to install updates
>>>>>> karlas-MacBook-Pro:~ karlagaldamez$ ./configure -macAccelerate clang
>>>>> -bash: ./configure: No such file or directory
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Karla M. Galdamez, Ph.D
>>>>> Affiliate Researcher
>>>>> Physics Department
>>>>> University of California at Berkeley
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> --
>>> Karla M. Galdamez, Ph.D
>>> Affiliate Researcher
>>> Physics Department
>>> University of California at Berkeley
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sat Jan 21 2017 - 01:30:02 PST
