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
>
--
Karla M. Galdamez, Ph.D
Affiliate Researcher
Physics Department
University of California at Berkeley
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Received on Fri Jan 20 2017 - 23:30:02 PST
