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mendesd Offline OP
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Hi,

I have no idea how to fix what is wrong with the build code or whatever. I ran the ./install.com osx and it executed perfectly (or so I think). So then I when into docs and read the cmake doc and tried to follow ./configure which I think executed fine. But when running 'make -j3' i get the errors that I attached in the txt file. I do not know what to do I have tried configuring and installing so many different ways to try and avoid this but nothing makes these errors go away/not occur.

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Make sure that you are using the most recent version.
Do not use install.com - this is an old installation method, which has been replaced by the ./configure (cmake) method; install in a clean file tree with no traces of previous installation attempts.


Lennart Nilsson
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mendesd Offline OP
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I did that I deleted the tar file from my computer and then downloaded it again giving me a fresh start and deleted and reinstalled GCC and gfortran. Both versions up to date and so is the tar file i do not know what to do after following the cmake.doc exactly with the correct options for configuring and I get the message that I attached when getting to the make command. I attached the error to see if anyone could help. Do I configure it in a separate directory? I just need to know what medications or things I need to fix for it to complete without errors.

Dylan Mendes
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That does seem like a very frustrating problem.

For me, those errors are just compiler warnings, and compilation continues until the end.

Can you tell me a little bit more about your setup:

Did you get free charmm or the full version?

What version of gfortran are you using?

Is it possible for you to remove the build/cmake subdirectory, try the configure command, and attach the output to a post as a text file?

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As you may have noticed, the CHARMM documentation is not very complete or up to date.

Here's what I've been doing successfully for years, and I just tested this on OS X Catalina:
  • obtain gcc from Xcode; verify via 'which gcc'
  • obtain and install gfortran (only) for your OS X version from hpc.sourceforge.net ; verify via 'which gfortran'
  • obtain and install CMake for OS X from cmake.org
  • on the 'configure' command line, include '--cmake /Applications/CMake.app/Contents/bin/cmake'


I usually do cmake builds in an empty parallel directory on OS X, so I invoke configure via e.g.

../c45b2/configure --cmake /Applications/CMake.app/Contents/bin/cmake

and then follow with 'make -j8'

Before configure, I used the first two steps above with the install.com build procedure, which usually worked.

Update for Big Sur

For OS X 11 (Big Sur) I had some problems initially, but after some updates to Xcode and the GCC suite at hpc.sourceforge.net, this minimalist approach is working again. The one change I had to make was to install the full GCC suite, instead of just gfortran, and use those C and C++ compilers (gcc, g++) for the CHARMM build. Xcode is only needed for the final link step, and these GCC compilers do that automatically.

Last edited by rmv; 06/29/21 06:12 PM. Reason: Big Sur update

Rick Venable
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mendesd Offline OP
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dyl:~ dylanmendes$ gfortran --version
GNU Fortran (Homebrew GCC 10.2.0_4) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

That is the version of gfortran that I am using.
I have the free version of charmm. Is the build/cmake directory in the charmm-build directory or in the charmm file that was uncompressed via terminal? In the charmm file that was uncompressed, the only subdirectory from build is UNX. When I configure and make -j3 into the charmm-build directory like it says in the cmake.info file I attached what happens.

I did the which for gcc and gfortran this is what it returned. I installed them from homebrew. Could you possibly elaborate more on exactly what I should do with install, configure and make? I also have mojave would that make a major difference?

dyl:charmm-build dylanmendes$ which gcc
/usr/bin/gcc
dyl:charmm-build dylanmendes$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 12.0.0 (clang-1200.0.32.29)
Target: x86_64-apple-darwin20.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
dyl:charmm-build dylanmendes$ which gfortran
/usr/local/bin/gfortran
dyl:charmm-build dylanmendes$ gfortran --version
GNU Fortran (Homebrew GCC 10.2.0_4) 10.2.0
Copyright (C) 2020 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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According to configure, cmake is not found and could not be built from scratch.

You can give configure the argument '--cmake <full path to the cmake command>' as rmv suggested.

You can install cmake using homebrew or use the binaries from here:
https://cmake.org/download/


Moderated by  lennart, rmv 

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