ncl installation on Mac with M1 chip and arm64 machine

[email-lhe]

Hi,

I'm using a new Mac with M1 chip and arm64 machine, while the precompiled ncl was based on old compilers are not eligible for new Mac that can't install old version compilers. I tried to compile it using new compilers on my Mac, a lot of issues came up because of updates of compilers. I wonder whether anyone has successfully installed ncl on Mac with M1 chip and arm64 machine and willing to share the precompiled code or the experience, so more people with new Macs can have access to it.

Some of my issues are about missing header files, even I have reinstalled the command line tools for several times.

/usr/X11R6/include/cairo/cairo-ft.h:46:10: fatal error: ft2build.h: No such file or directory
46 | #include <ft2build.h>

hdf.c:54:10: fatal error: hdf.h: No such file or directory
54 | #include <hdf.h>

/Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/signal.h:69:42: error: 'NSIG' undeclared here (not in a function)
69 | extern __const char *__const sys_signame[NSIG];
| ^~~~

udunitsW.c:5:10: fatal error: udunits2.h: No such file or directory
5 | #include <udunits2.h>

NclGRIB2.h:1:10: fatal error: grib2.h: No such file or directory
1 | #include <grib2.h>

NclApi.c:39:10: fatal error: netcdf.h: No such file or directory
39 | #include <netcdf.h>

udunitsW.c:5:10: fatal error: udunits2.h: No such file or directory
5 | #include <udunits2.h>

LDFLAGS="-L/usr/local/opt/freetype/lib -L/usr/local/opt/libpng/lib" CPPFLAGS="-I/usr/local/opt/freetype/include -I/usr/local/opt/libpng/include -I/usr/local/opt/freetype/include/freetype2" pip install matplotlib

LDFLAGS="-L/opt/X11/lib -L/usr/local/opt/libpng/lib" CPPFLAGS="-I/opt/X11/include/freetype2"

I would appreciate any help, thanks in advance.

Best,
Lynn

[rbrownrigg]

Hi, I've never tried to build for the M1 architecture. However, all of those missing headers are from libraries NCL depends on. I don't understand the context of these two lines: LDFLAGS="-L/usr/local/opt/freetype/lib -L/usr/local/opt/libpng/lib" CPPFLAGS="-I/usr/local/opt/freetype/include -I/usr/local/opt/libpng/include -I/usr/local/opt/freetype/include/freetype2" pip install matplotlib LDFLAGS="-L/opt/X11/lib -L/usr/local/opt/libpng/lib" CPPFLAGS="-I/opt/X11/include/freetype2" Namely, 1st line -- what does a pip install of matplotlib have to do with building NCL sources? And 2nd line -- there's an include directive for freetype -- what about all the other library headers like netcdf, grib2, udunits, etc.? These are the build instructions, including all dependencies: http://ncl.ucar.edu/Download/build_from_src.shtml Good luck! Rick

…

On Fri, Jun 3, 2022 at 11:36 AM Liyuan He ***@***.***> wrote: Hi, I'm using a new Mac with M1 chip and arm64 machine, while the precompiled ncl was based on old compilers are not eligible for new Mac that can't install old version compilers. I tried to compile it using new compilers on my Mac, a lot of issues came up because of updates of compilers. I wonder whether anyone has successfully installed ncl on Mac with M1 chip and arm64 machine and willing to share the precompiled code or the experience, so more people with new Macs can have access to it. Some of my issues are about missing header files, even I have reinstalled the command line tools for several times. /usr/X11R6/include/cairo/cairo-ft.h:46:10: fatal error: ft2build.h: No such file or directory 46 | #include <ft2build.h> hdf.c:54:10: fatal error: hdf.h: No such file or directory 54 | #include <hdf.h> /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk/usr/include/signal.h:69:42: error: 'NSIG' undeclared here (not in a function) 69 | extern __const char *__const sys_signame[NSIG]; | ^~~~ udunitsW.c:5:10: fatal error: udunits2.h: No such file or directory 5 | #include <udunits2.h> NclGRIB2.h:1:10: fatal error: grib2.h: No such file or directory 1 | #include <grib2.h> NclApi.c:39:10: fatal error: netcdf.h: No such file or directory 39 | #include <netcdf.h> udunitsW.c:5:10: fatal error: udunits2.h: No such file or directory 5 | #include <udunits2.h> LDFLAGS="-L/usr/local/opt/freetype/lib -L/usr/local/opt/libpng/lib" CPPFLAGS="-I/usr/local/opt/freetype/include -I/usr/local/opt/libpng/include -I/usr/local/opt/freetype/include/freetype2" pip install matplotlib LDFLAGS="-L/opt/X11/lib -L/usr/local/opt/libpng/lib" CPPFLAGS="-I/opt/X11/include/freetype2" I would appreciate any help, thanks in advance. Best, Lynn — Reply to this email directly, view it on GitHub <#187>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADLWOXVHOIIKOJUISZX65UTVNI7BZANCNFSM5XZVSDYQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[MicroTed]

@email-lhe Did you have any success with this? I managed to at least compile the ncar graphics libraries, which I wanted for an old fortran plotting program. NCL works fine in emulation, but I'll see if I can get that to compile, as well (without hdf4 and some other options for now). The freetype error is fixed by adding it to the include paths (e.g., the Darwin_Arm config file in my fork)

My fork is https://github.com/MicroTed/ncl.git branch apple-arm64

I installed most of the dependencies with homebrew, and am using gcc-12 (also from homebrew). gcc apparently does not compile using xcode 14, so I'm using 13.4.1. I have netcdf4 compiled separately (netcdf-4.9.0).

It built an ncl executable, but that hits a seg fault somewhere quickly and fails.

[Dave-Allured]

Macports is reportedly building M1/arm64 versions from source. You might give that a try. If it works, please let us know, including your OS and Xcode versions.

https://ports.macports.org/port/ncarg/details/

[MicroTed]

Thanks for the news on that. I tried installing it on my M1 macbook pro. It compiles and creates arm64 binaries:

/opt/local/bin/ncl: Mach-O 64-bit executable arm64

but ncl gives a seg fault:

% ncl gsun01n.ncl
Copyright (C) 1995-2019 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.6.2
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
Segmentation fault: 11

The libraries might work, e.g., for linking to fortran, but I haven't tried that yet (and that part was working before, too).

It's really just the calling fortran from C that needs help at this point. That is the source of the seg fault because the fortran side (CPNUMB) thinks a string is a lot longer than it really is and tries to initialize it. I haven't had time to learn how to fix that.

-- Ted

[zarzycki]

Macports is reportedly building M1/arm64 versions from source. You might give that a try. If it works, please let us know, including your OS and Xcode versions.

https://ports.macports.org/port/ncarg/details/

FYI, I appear to have successfully built an arm64 version of NCL using MacPorts. No extensive testing, but can generate graphics successfully using some of the sample scripts. I have similar issues as @MicroTed with homebrew. Did not try building from source.

% file /opt/local/bin/ncl
/opt/local/bin/ncl: Mach-O 64-bit executable arm64

with

export NCARG_ROOT=/opt/local
## Did not need this after switch to bash + reboot
## export DISPLAY=:0.0

in my .profile.

Process for me was simple, install MacPorts following instructions here and then:

sudo port install ncarg

Took about ~15-20 minutes.

MacOS 13.2.1
M1 Max

[tenomoto]

I am the maintainer of ncarg in MacPorts. Thanks to @MicroTed and my student I am aware of segfault. I ran all the examples and found that text, colour bars, and maps works, but not xy and contour plots. ncargex seems to work so it should be a problem with NCL or depending libraries. I still get segfault even with the workaround suggested by @MicroTed and am investigating the issue.

[tenomoto]

I got segfault with C/Fortran as well when hlu is used. The failure occurs when NhlCreate() is called at line 151 in xy01c.c with NhlxyPlotClass. ni/src/lib/hlu/XyPlot.c does not seem to call cpnumb at least directly. https://www.ncl.ucar.edu/Applications/BasicExamples/XyPlot/xy01.shtml

A minimum example in NCL would be:

begin
  wkn = "xy"
  wks = gsn_open_wks("x11", wkn)
  plot_object = create wkn xyPlotClass wks
  end create
end

[tenomoto]

I built ncl on FreeBSD arm64/UTM and had same error. The stack trace in the dumped core indicates an issue with len_trim.

#0  0x00000000433798a8 in _gfortran_string_len_trim () from /usr/local/lib/gcc12/libgfortran.so.5

[zarzycki]

Yes, I can reproduce I get the same behavior @tenomoto notes. NCL compiles and runs some scripts/code fine but then segfaults elsewhere. Using xy_2.ncl example...

$ ncl xy_2.ncl 
 Copyright (C) 1995-2019 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.6.2
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)	data created, generating xy plot
Segmentation fault: 11

[Dave-Allured]

@tenomoto, please show more of that stack trace. Rebuild ncarg with -g, if necessary to add ncarg symbols to the stack trace, so that we can better understand the context. Len_trim is called only from fortran code, so this should be traceable back into ncarg source code.

[tenomoto]

I haven't tried on macOS, but on FreeBSD len_trim is everything I get even with -g option.

[Dave-Allured]

Okay. I do not find a direct call to len_trim, anywhere in NCL 6.6.2 source code, or in current Macports patches. Either it is called by a dependency, or else the stack or execution sequence is broken.

[MicroTed]

Is it the same as calling 'len', e.g., len(cbuf)? Although I found that it returned a faulty value, the seg fault occured when cpnumb tried to set cbuf to blanks: cbuf=' ' or cbuf(1:lbuf)=' ' (with faulty lbuf from len)

[email-lhe]

@email-lhe Did you have any success with this? I managed to at least compile the ncar graphics libraries, which I wanted for an old fortran plotting program. NCL works fine in emulation, but I'll see if I can get that to compile, as well (without hdf4 and some other options for now). The freetype error is fixed by adding it to the include paths (e.g., the Darwin_Arm config file in my fork)

My fork is https://github.com/MicroTed/ncl.git branch apple-arm64

I installed most of the dependencies with homebrew, and am using gcc-12 (also from homebrew). gcc apparently does not compile using xcode 14, so I'm using 13.4.1. I have netcdf4 compiled separately (netcdf-4.9.0).

It built an ncl executable, but that hits a seg fault somewhere quickly and fails.

Sorry for the late response. Not yet. I used python instead.

[Dave-Allured]

Is it the same as calling 'len', e.g., len(cbuf)? ...

No, len() returns the declared length of a fortran character string. Len_trim() returns the string length, minus any trailing blanks. It is possible that len_trim() would call len() internally, but not the reverse.

If len(cbuf) returned a faulty value that exceeded the string length, then cbuf(1:lbuf)=' ' would possibly cause seg fault. However, bad value from len(cbuf) is concerning by itself.