First Jamie, thanks for all your hard work on the cmake build. It
really is amazing especially given the highly decentralized codebase
that is Amber.
On Mon, Apr 5, 2021 at 2:50 PM Jamie Smith
<jsmith.crackofdawn.onmicrosoft.com> wrote:
>
> For what it's worth, CMake should autodetect and use external libraries like NetCDF without you having to do anything that verbose. Was it installed to a location that was not in your system directories (e.g. /usr)?
This was in an HPC environment containing multiple compilers and
compiler-specific library builds. This one was in something like
'/v/apps/netcdf3/gcc_7.5.0'.
> If so, there's a much more straightforward way to do what you did: use CMAKE_PREFIX_PATH. Passing this option (e.g. -DCMAKE_PREFIX_PATH=<my/dir>) causes CMake to scan the include/ and lib/ directories of the given directory for libraries in addition to the regular system search path. It's equivalent to the Autoconf "--prefix" option if you've used that (except it doesn't change the install dir). What I like to do is install all my dependency libraries to a single prefix and then use that option so that it can find them.
What if say e.g. I want to use an external NetCDF from somewhere like
'/usr/lib' but that directory also contains FFTW - would cmake then
use the FFTW as well? What if I want the external NetCDF but not FFTW?
It would be nice to be able to fine-tune things with the PREFIX_PATH
style, but have different variables for different external components,
e.g. '-DNETCDF_PREFIX_PATH' etc.
-Dan
>
> Jamie
>
> -----Original Message-----
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Monday, April 5, 2021 11:41 AM
> To: AMBER Developers Mailing List <amber-developers.ambermd.org>
> Subject: Re: [AMBER-Developers] CMake in Amber
>
> Hi All,
>
> I heartily agree with Adrian - the documentation for cmake needs to be
> *vastly* improved, and also centralized if at all possible. I ran into headaches with cmake documentation recently, details below.
>
> On Mon, Apr 5, 2021 at 12:50 PM David A Case <david.case.rutgers.edu> wrote:
> >
> > We are using the wiki rather than a --help option for this purpose.
> > Two pages are good starting points:
> >
> > https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Quick-Start
> >
> > is a good overview. It has an FAQ with answers to questions such as
> > "How can I build only one specific program?" or "I want to see what
> > commands make is actually executing!"
> >
> > Also very helpful is this one:
> >
> > https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
>
> These pages are good, but they are also incomplete. Recently, I was trying to figure out how to specify an external NetCDF library (with configure, accomplished using '--with-netcdf=$netcdf_home'). There is no specific option for cmake given, but the text at the bottom of the "Common Options" wiki page indicates (talking about the old configure flag -netcdfstatic):
>
> "-netcdfstatic -- Just change NETCDF_LIBRARIES_C, NETCDF_LIBRARIES_F77, and NETCDF_LIBRARIES_F90 to point to static libraries."
>
> This actually **does not work** for specifying an external NetCDF.
> Cmake will complain about "Failed to find NetCDF interface for F77/F90". The manual has a few additional breadcrumbs (in 2.2.3): it mentions specifying the location of parallel NetCDF:
>
> ```
> For example, if you saw this output:
> -- Could NOT find PnetCDF_C (missing: PnetCDF_C_LIBRARY PnetCDF_C_INCLUDE_DIR) you could help CMake find the library with the following command:
> cmake <path to source> -DPnetCDF_C_LIBRARY=<path to libpnetcdf.so> \
> -DPnetCDF_C_INCLUDE_DIR=<path to folder containing pnetcdf.h> ```
>
> Using this as a hint, and diving into the cmake scripts for the actual variable names, I figured out I could specify an external NetCDF file via the CMAKE variables:
>
> -DNetCDF_LIBRARIES_C=$netcdf_home/lib/libnetcdf.a \
> -DNetCDF_INCLUDES=$netcdf_home/include \
> -DNetCDF_LIBRARIES_F77=$netcdf_home/lib/libnetcdff.a \
> -DNetCDF_LIBRARIES_F90=$netcdf_home/lib/libnetcdff.a \
> -DNetCDF_INCLUDES_F90=$netcdf_home/include \
> -DNetCDF_INCLUDES_F77=$netcdf_home/include
>
> This took some dedicated sleuthing on my part, and I'm a long-time developer. I don't think users shouldn't have to jump through these hoops.
>
> > p.p.s. Note that the current output of configure --help is 54 lines
> > long, and that of configure --full-help (which is needed to get help
> > for any but the most elementary subjects) is 154 lines.
>
> Be that as it may, whenever I had a question on how to build amber, 99 times out of 100 I could do './configure --full-help | less` and have a one-stop shop of options and what they do, and then figure out what I needed to set. So I very much second Adrian's suggestion that there be a single location where all configurable cmake options are listed.
> Whether that is a wiki page, a page in the manual, or some sort of onboard help program I don't particularly care. I just don't want to have to dive all over wiki pages, then the manual, then into the guts of cmake every time I want to change a default. Also, having a single source will make keeping that documentation up-to-date feasible.
>
> -Dan
>
> >
> > This shows you how to ask for the most common changes, such as how to
> > skip certain builds, change what libraries are used, change compiler flags, etc.
> >
> > If you look at the table of contents at the left of any of these
> > pages, you will see several other CMake related pages.
> >
> > For everyone: please note that these are wiki pages! If there is
> > something that is unclear, or is missing, please edit things to make them better.
> >
> > ...hope this helps....dac
> >
> > p.s. the links above are printed out at the very beginning of every
> > CMake run. See also Section 2.2 of the Amber Reference Manual.
> >
> > p.p.s. Note that the current output of configure --help is 54 lines
> > long, and that of configure --full-help (which is needed to get help
> > for any but the most elementary subjects) is 154 lines. Also note
> > that things like compiler info in the help output are 4-5 years out of
> > date, and other pieces of information in the current help output are
> > also wrong or misleading. So, in my view, using a wiki is a better
> > way to make things easy to read, and to keep them up to date.
> >
> > Finally, the current configure help doesn't even try to answer
> > Adrian's question about "building some things but not others". The
> > answer for the legacy configure system is this "find the relevant Makefile, and edit it."
> > For CMake, you add an option to your run_cmake script.
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Mon Apr 05 2021 - 12:30:02 PDT
