Hello,

I have been trying to run the python notebook tutorial and am running into some issues. Below are the details:

Python 3.9.12 MacOS Ventura 13.0.1

We are running the 2nd cell:

MPI version: comment this out if you don't have an OpenMPI-enabled compiler (e.g. mpif90)

earth = exo.Model(workdir="earth",modelname="earth",resolution="T21",ncpus=4,layers=10,precision=8)

Single-core version: uncomment if you don't have OpenMPI

earth = exo.Model(workdir="earth",modelname="earth",resolution='T21',ncpus=1,layers=10,precision=8)

This is the output I am getting:

mkdir: /Users/chasealvaradoanderson/Desktop/exomodel/earth/: File exists rm: plasim.x: No such file or directory rm: ../bin/most_plasim_t21_l10_p1.x: No such file or directory rm: ../run/most_plasim_t21_l10_p1.x: No such file or directory cp: ../src/specs is a directory (not copied). Checking for /Users/chasealvaradoanderson/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/plasim/run/most_plasim_t21_l10_p1.x.... PRODUCING: -r8 -o most_plasim_t21_l10_p1.x Writing resmod.f90..... Writing makefile...

gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 resmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 plasimmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 mpimod_stub.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 fftmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 specblock.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 radmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 oceanmod.f90 oceanmod.f90:237:31:

235 | do jlev=1,nlem_oce | 2
...... 238 | & /(dlayer(jlev)+dlayer(jlev+1)) | 1 Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2) gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 icemod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 seamod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 cpl_stub.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 guimod_stub.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 rainmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 landmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 simba.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 p_earth.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 carbonmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 hurricanemod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 utilities_stub.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 plasim.f90 plasim.f90:1534:16:

1532 | do jlev=NLEV-10,NLEV | 2 1533 | zsk=REAL(jlev-(NLEV-9+1))/10.0 !As if it was a 10-layer atmosphere 1534 | sigmah(jlev)=0.75zsk+1.75zsk3-1.5*zsk*4 | 1 Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2) gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 calmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 gaussmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 legmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 glaciermod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 outmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 miscmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 fluxmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 surfmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 restartmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 tracermod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 tpcore.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 trc_routines.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 aeromod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 aerocore.f90 gcc -c -O3 pumax_stub.c gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 lsgmod.f90 gfortran -o plasim.x -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero mpimod_stub.o fftmod.o guimod_stub.o rainmod.o simba.o p_earth.o carbonmod.o hurricanemod.o utilities_stub.o resmod.o plasim.o plasimmod.o specblock.o calmod.o gaussmod.o legmod.o outmod.o miscmod.o fluxmod.o radmod.o surfmod.o landmod.o glaciermod.o seamod.o icemod.o oceanmod.o restartmod.o tracermod.o tpcore.o trc_routines.o aeromod.o aerocore.o pumax_stub.o lsgmod.o cpl_stub.o ld: warning: ignoring file pumax_stub.o, building for macOS-arm64 but attempting to link with file built for unknown-x86_64 Undefined symbols for architecture arm64: "nresources", referenced from: epilog in plasim.o ld: symbol(s) not found for architecture arm64 collect2: error: ld returned 1 exit status make: [plasim.x] Error 1 cp: plasim.x: No such file or directory cp: ../bin/most_plasim_t21_l10_p1.x: No such file or directory cp: /Users/chasealvaradoanderson/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/plasim/run/most_plasim_t21_l10_p1.x: No such file or directory

It seems like the file 'most_plasim_t21_l10_p1.x' is not created, but I can still run the earth.config() & earth.exportcfg() commands. When trying to run the following earth simulation, 'earth.run(years=1,clean=False) #clean=False leaves the original output file in place', I am getting the following error:

Command '['./most_plasim_t21_l10_p1.x']' returned non-zero exit status 127.

CalledProcessError Traceback (most recent call last) File ~/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/init.py:1051, in Model._run(self, years, postprocess, crashifbroken, clean) 1050 elif float(sys.version[:3])>=3.7: -> 1051 subprocess.run([self._exec+self.executable],shell=True,check=True, 1052 capture_output=True) 1053 else:

File ~/opt/anaconda3/lib/python3.9/subprocess.py:528, in run(input, capture_output, timeout, check, *popenargs, **kwargs) 527 if check and retcode: --> 528 raise CalledProcessError(retcode, process.args, 529 output=stdout, stderr=stderr) 530 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '['./most_plasim_t21_l10_p1.x']' returned non-zero exit status 127.

During handling of the above exception, another exception occurred:

RuntimeError Traceback (most recent call last) /Users/chasealvaradoanderson/Desktop/exomodel/exoplasim_tutorial.ipynb Cell 6 in () ----> 1 earth.run(years=1,clean=False)

File ~/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/init.py:613, in Model.run(self, *kwargs) 594 """Run the Model's designated run routine. 595 ... 1987 os.system("mv %s/ %s_crashed/"%(self.secondarydir,self.crashdir)) 1988 os.system("mv %s/* %s_crashed/"%(self.workdir,self.crashdir)) -> 1989 raise RuntimeError("ExoPlaSim has crashed or begun producing garbage. All working files have been moved to %s_crashed/"%(os.getcwd()+"/"+self.modelname))

RuntimeError: ExoPlaSim has crashed or begun producing garbage. All working files have been moved to /Users/chasealvaradoanderson/Desktop/exomodel/earth_crashed/

It seems like this error is connected to the previous one, in that the file './most_plasim_t21_l10_p1.x' is not being found. Is this a package related error, or something wrong on my end?

Thanks!

This is because you're using an arm64 Mac OS, i.e. one with an M1 chip or newer. The ARM architecture is extremely breaking for an awful lot of things in scientific computing, and ExoPlaSim is not tested on it nor guaranteed to be compatible with it. Looks like it isn't. This is on the roadmap for the future, but it likely won't happen anytime soon, because it requires extensive testing on very specific hardware. In the meantime, try deleting references to pumax in the exoplasim/plasim/src/make_plasim file (in the directory where exoplasim got installed to), and then try compiling. pumax is the GUI for PlaSim, which isn't really used much anymore (and may not work at the moment, for all I know). There may be other far more fundamental things that break on Apple silicon, particularly as relates to abandoning support for 32-bit variables, but you can go ahead and see if just axing pumax does the trick.

On Mon, Aug 5, 2024 at 6:17 PM Chase-astro01 @.***> wrote:

Hello,

I have been trying to run the python notebook tutorial and am running into some issues. Below are the details:

Python 3.9.12 MacOS Ventura 13.0.1

We are running the 2nd cell:

MPI version: comment this out if you don't have an OpenMPI-enabled

compiler (e.g. mpif90) earth = exo.Model(workdir="earth",modelname="earth",resolution="T21",ncpus=4,layers=10,precision=8)

Single-core version: uncomment if you don't have OpenMPI

earth = exo.Model(workdir="earth",modelname="earth",resolution='T21',ncpus=1,layers=10,precision=8)

This is the output I am getting:

mkdir: /Users/chasealvaradoanderson/Desktop/exomodel/earth/ https://file+.vscode-resource.vscode-cdn.net/Users/chasealvaradoanderson/Desktop/exomodel/earth/: File exists rm: plasim.x: No such file or directory rm: ../bin/most_plasim_t21_l10_p1.x: No such file or directory rm: ../run/most_plasim_t21_l10_p1.x: No such file or directory cp: ../src/specs is a directory (not copied). Checking for /Users/chasealvaradoanderson/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/plasim/run/most_plasim_t21_l10_p1.x.... https://file+.vscode-resource.vscode-cdn.net/Users/chasealvaradoanderson/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/plasim/run/most_plasim_t21_l10_p1.x.... PRODUCING: -r8 -o most_plasim_t21_l10_p1.x Writing resmod.f90..... Writing makefile...

gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 resmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 plasimmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 mpimod_stub.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 fftmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 specblock.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 radmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 oceanmod.f90 oceanmod.f90:237:31:

235 | do jlev=1,nlem_oce | 2 236 | vdiffk(jlev)=(dlayer(jlev)vdiffkl(jlev) & 237 | & +dlayer(jlev+1)vdiffkl(jlev+1)) & | 1 Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2) oceanmod.f90:237:47:

235 | do jlev=1,nlem_oce | 2 236 | vdiffk(jlev)=(dlayer(jlev)vdiffkl(jlev) & 237 | & +dlayer(jlev+1)vdiffkl(jlev+1)) & | 1 Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2) oceanmod.f90:238:44:

235 | do jlev=1,nlem_oce | 2 ...... 238 | & / https://file+.vscode-resource.vscode-cdn.net/ (dlayer(jlev)+dlayer(jlev+1)) | 1 Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2) gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 icemod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 seamod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 cpl_stub.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 guimod_stub.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 rainmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 landmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 simba.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 p_earth.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 carbonmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 hurricanemod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 utilities_stub.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 plasim.f90 plasim.f90:1534:16:

1532 | do jlev=NLEV-10,NLEV | 2 1533 | zsk=REAL(jlev-(NLEV-9+1))/10.0 !As if it was a 10-layer atmosphere 1534 | sigmah(jlev)=0.75zsk+1.75zsk3-1.5zsk4 | 1 Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2) gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 calmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 gaussmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 legmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 glaciermod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 outmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 miscmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 fluxmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 surfmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 restartmod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 tracermod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 tpcore.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 trc_routines.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 aeromod.f90 gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 aerocore.f90 gcc -c -O3 pumax_stub.c gfortran -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 lsgmod.f90 gfortran -o plasim.x -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero mpimod_stub.o fftmod.o guimod_stub.o rainmod.o simba.o p_earth.o carbonmod.o hurricanemod.o utilities_stub.o resmod.o plasim.o plasimmod.o specblock.o calmod.o gaussmod.o legmod.o outmod.o miscmod.o fluxmod.o radmod.o surfmod.o landmod.o glaciermod.o seamod.o icemod.o oceanmod.o restartmod.o tracermod.o tpcore.o trc_routines.o aeromod.o aerocore.o pumax_stub.o lsgmod.o cpl_stub.o ld: warning: ignoring file pumax_stub.o, building for macOS-arm64 but attempting to link with file built for unknown-x86_64 Undefined symbols for architecture arm64: "nresources", referenced from: epilog* in plasim.o ld: symbol(s) not found for architecture arm64 collect2: error: ld returned 1 exit status make: *** [plasim.x] Error 1 cp: plasim.x: No such file or directory cp: ../bin/most_plasim_t21_l10_p1.x: No such file or directory cp: /Users/chasealvaradoanderson/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/plasim/run/most_plasim_t21_l10_p1.x https://file+.vscode-resource.vscode-cdn.net/Users/chasealvaradoanderson/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/plasim/run/most_plasim_t21_l10_p1.x: No such file or directory

It seems like the file 'most_plasim_t21_l10_p1.x' is not created, but I can still run the earth.config() & earth.exportcfg() commands. When trying to run the following earth simulation, 'earth.run(years=1,clean=False)

clean=False leaves the original output file in place', I am getting the

following error: Command '['./most_plasim_t21_l10_p1.x']' returned non-zero exit status 127.

CalledProcessError Traceback (most recent call last) File ~/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/ init.py:1051 https://file+.vscode-resource.vscode-cdn.net/Users/chasealvaradoanderson/Desktop/exomodel/~/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/__init__.py:1051, in Model._run(self, years, postprocess, crashifbroken, clean) 1050 elif float(sys.version[:3])>=3.7: -> 1051 subprocess.run([self._exec+self.executable],shell=True,check=True, 1052 capture_output=True) 1053 else:

File ~/opt/anaconda3/lib/python3.9/subprocess.py:528 https://file+.vscode-resource.vscode-cdn.net/Users/chasealvaradoanderson/Desktop/exomodel/~/opt/anaconda3/lib/python3.9/subprocess.py:528, in run(input, capture_output, timeout, check, *popenargs, **kwargs) 527 if check and retcode: --> 528 raise CalledProcessError(retcode, process.args, 529 output=stdout, stderr=stderr) 530 return CompletedProcess(process.args, retcode, stdout, stderr)

CalledProcessError: Command '['./most_plasim_t21_l10_p1.x']' returned non-zero exit status 127.

During handling of the above exception, another exception occurred:

RuntimeError Traceback (most recent call last) /Users/chasealvaradoanderson/Desktop/exomodel/exoplasim_tutorial.ipynb https://file+.vscode-resource.vscode-cdn.net/Users/chasealvaradoanderson/Desktop/exomodel/exoplasim_tutorial.ipynb Cell 6 in () ----> 1 earth.run(years=1,clean=False)

File ~/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/ init.py:613 https://file+.vscode-resource.vscode-cdn.net/Users/chasealvaradoanderson/Desktop/exomodel/~/opt/anaconda3/lib/python3.9/site-packages/exoplasim-3.4.0-py3.9.egg/exoplasim/__init__.py:613, in Model.run(self,

kwargs) 594 """Run the Model's designated run routine. 595 ... 1987 os.system("mv %s/ https://file+.vscode-resource.vscode-cdn.net/ %s_crashed/"%(self.secondarydir,self.crashdir)) 1988 os.system("mv %s/ https://file+.vscode-resource.vscode-cdn.net/ %s_crashed/"%(self.workdir,self.crashdir)) -> 1989 raise RuntimeError("ExoPlaSim has crashed or begun producing garbage. All working files have been moved to %s_crashed/"%(os.getcwd()+"/ https://file+.vscode-resource.vscode-cdn.net/"+self.modelname))

RuntimeError: ExoPlaSim has crashed or begun producing garbage. All working files have been moved to /Users/chasealvaradoanderson/Desktop/exomodel/earth_crashed/ https://file+.vscode-resource.vscode-cdn.net/Users/chasealvaradoanderson/Desktop/exomodel/earth_crashed/

It seems like this error is connected to the previous one, in that the file './most_plasim_t21_l10_p1.x' is not being found. Is this a package related error, or something wrong on my end?

Thanks!

— Reply to this email directly, view it on GitHub https://github.com/alphaparrot/ExoPlaSim/issues/33, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADRQKQCW4UKFZSE5GSKZA5DZP72YFAVCNFSM6AAAAABMBDV6T2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ2DSNJWHE4DIMI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

@alphaparrot I may get a computer just to run ExoPlaSim simulations for a world building project and was wondering: should I try to maximize core and/or thread count or maximize RAM? Or any other thing? I'd like to run at T170 (already figure I should maximize storage) but so far have consistently failed to run ExoPlaSim.

Most advice online seems to indicate maximizing RAM is best, but since ExoPlaSim explicitly asks for your core count wanted to check.

Thanks in advance.

Maximize core count and the speed of each processing unit. At T170 RAM is a concern, yes, but T170 is slow. VERY slow. You are going to need every ounce of parallelism you can get. Running on a decent Intel Xeon supercomputing chip with 64 cores about 5 years ago, I saw at best maybe 1 year of simulated climate per day of wall-time. Don't skimp on disk space either; depending on how much output you capture (especially high-cadence output), a T170 run can generate well over 1 GB of data per simulated year.

I will warn you that by necessity ExoPlaSim is not well-tested at T170, and this is high enough resolution that there's likely greater sensitivity to the physics that ExoPlaSim treats in a more simplified, parameterized manner, especially cloud microphysics. I don't expect ExoPlaSim to get clouds right at extremely high resolution. Hurricane generation is also very likely wrong. And at these resolutions, you will definitely see the impact of not having a dynamic ocean with ocean currents (a deficit common to all atmosphere-only GCMs at high resolutions).

I would strongly recommend, before you spend the equivalent of a new car on computing hardware, evaluating why you need T170. I went to T170 because I wanted to take a stab at hurricanes, and I needed sub-100km resolution to do it. That also necessitated high-cadence output, as storms are short-lived. When it comes to regional climate, you very likely don't need resolution this extreme. You may get equally satisfying and much cheaper and faster results by running at lower resolution and then interpolating/extrapolating the output to a higher resolution. This would be a good task for a generative AI of some kind. I believe Nikolai Hersfeldt has a script for extrapolating surface temperatures for higher-resolution topographic maps, though I could be wrong about who pulled that off.

On Wed, Aug 7, 2024, 5:00 AM Rhombus55 @.***> wrote:

@alphaparrot https://github.com/alphaparrot I may get a computer just to run ExoPlaSim simulations for a world building project and was wondering: should I try to maximize core and/or thread count or maximize RAM? Or any other thing? I'd like to run at T170 (already figure I should maximize storage) but so far have consistently failed to run ExoPlaSim.

Most advice online seems to indicate maximizing RAM is best, but since ExoPlaSim explicitly asks for your core count wanted to check.

Thanks in advance.

— Reply to this email directly, view it on GitHub https://github.com/alphaparrot/ExoPlaSim/issues/33#issuecomment-2272975704, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADRQKQDPVSYAEGYDLHXJ3BLZQHO2ZAVCNFSM6AAAAABMBDV6T2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZSHE3TKNZQGQ . You are receiving this because you were mentioned.Message ID: @.***>

@alphaparrot Thanks! This has been extremely insightful.

Hi @alphaparrot ,

I am having some issues executing and running the model. I switched from running directly on my mac to my institution's HPC, so that seemed to have resolved some of the issues. I was able to get the earth model to run, but have not been unable to run the proximab or toi700d models. The earth model finally ran after I completely scrapped and remade my virtual environment with more careful installations and module loads. All of the cells up until the actual run seem to run fine. Below I have pasted the input and outputs from my terminal's virtual environment:

Proximab:

proxb = exo.TLaquaplanet(workdir="proximab",modelname="proxima_b",resolution='T21',layers=10,ncpus=4,precision=8,outputtype='.nc') Checking for /home/users/chasekaa/exomodel/exo_env/lib/python3.9/site-packages/exoplasim/plasim/run/most_plasim_t21_l10_p4.x....

proxb.configure(startemp=3000.0, flux=1300.0,rotationperiod=11.2) Mean Molecular Weight set to 28.9703 g/mol rm: cannot remove ‘/home/users/chasekaa/exomodel/proximab/plasim_restart’: No such file or directory proxb.exportcfg() Writing configuration.... 1 1300.0 3000.0 None

287.0000002469167 1.011 1 0 11.2 1 180.0 None 9.80665 1.0 0.0 0.0 None 1 None 1 0 0 gp|exp|sp 8.0 8 15.0 None None None None None None None 50.0 None 0 None None None ECHAM-3 0 None 1 0 None 0 0 None 1.0 50.0 None None 0 None 30.0 None None toggle|0&start|320&end|576&interval|4 720

None 0&2.0&-1.0 0.0005 0.0 None None 0.0 0 1 1.0 0.5 1.0 2.0 0.0 0.0 1.0 0 None 0 5e-09 1 1000.0 1e-12 1 1 None Writing to /home/users/chasekaa/exomodel/proximab/proxima_b.cfg....

proxb.cfgpostprocessor(ftype='regular',extension='.nc',mode='synchronous',physfilter=True) proxb.cfgpostprocessor(ftype='snapshot',extension='.nc',mode='synchronous',physfilter=True) proxb.run(clean=False) Command '['mpiexec -np 4 --use-hwthread-cpus most_plasim_t21_l10_p4.x']' returned non-zero exit status 1. Traceback (most recent call last): File "/home/users/chasekaa/exomodel/exo_env/lib/python3.9/site-packages/exoplasim/init.py", line 1051, in _run subprocess.run([self._exec+self.executable],shell=True,check=True, File "/share/software/user/open/python/3.9.0/lib/python3.9/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['mpiexec -np 4 --use-hwthread-cpus most_plasim_t21_l10_p4.x']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "/home/users/chasekaa/exomodel/exo_env/lib/python3.9/site-packages/exoplasim/init.py", line 613, in run self._run(**kwargs) File "/home/users/chasekaa/exomodel/exo_env/lib/python3.9/site-packages/exoplasim/init.py", line 1147, in _run self._crash() #Bring in the cleaners File "/home/users/chasekaa/exomodel/exo_env/lib/python3.9/site-packages/exoplasim/init.py", line 1989, in _crash raise RuntimeError("ExoPlaSim has crashed or begun producing garbage. All working files have been moved to %s_crashed/"%(os.getcwd()+"/"+self.modelname)) RuntimeError: ExoPlaSim has crashed or begun producing garbage. All working files have been moved to /home/users/chasekaa/exomodel/proxima_b_crashed/

Toi700d:

toi700d = exo.Model(workdir="toi700d_run",modelname="TOI-700d", ... ncpus=4,resolution="T21",outputtype=".npz") Checking for /home/users/chasekaa/exomodel/exo_env/lib/python3.9/site-packages/exoplasim/plasim/run/most_plasim_t21_l10_p4.x.... PRODUCING: -r8 -o most_plasim_t21_l10_p4.x Writing resmod.f90..... rm: cannot remove ‘plasim.x’: No such file or directory rm: cannot remove ‘../bin/most_plasim_t21_l10_p4.x’: No such file or directory rm: cannot remove ‘../run/most_plasim_t21_l10_p4.x’: No such file or directory cp: omitting directory ‘../src/specs’ Writing makefile...

mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 resmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 plasimmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 mpimod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 fftmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 specblock.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 radmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 oceanmod.f90 oceanmod.f90:237:31:

235 | do jlev=1,nlem_oce | 2
...... 238 | & /(dlayer(jlev)+dlayer(jlev+1)) | 1 Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2) mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 icemod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 seamod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 cpl_stub.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 guimod_stub.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 rainmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 landmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 simba.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 p_earth.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 carbonmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 hurricanemod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 utilities.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 plasim.f90 plasim.f90:1534:16:

1532 | do jlev=NLEV-10,NLEV | 2 1533 | zsk=REAL(jlev-(NLEV-9+1))/10.0 !As if it was a 10-layer atmosphere 1534 | sigmah(jlev)=0.75zsk+1.75zsk*3-1.5zsk**4 | 1 Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2) mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 calmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 gaussmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 legmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 glaciermod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 outmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 miscmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 fluxmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 surfmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 restartmod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 tracermod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 tpcore.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 trc_routines.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 aeromod.f90 mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 aerocore.f90 mpicc -c -O3 pumax_stub.c mpif90 -c -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero -fdefault-real-8 lsgmod.f90 mpif90 -o plasim.x -O3 -cpp -fcheck=all -ffixed-line-length-132 -ffpe-trap=invalid,zero,overflow -ffpe-summary=none -finit-real=zero mpimod.o fftmod.o guimod_stub.o rainmod.o simba.o p_earth.o carbonmod.o hurricanemod.o utilities.o resmod.o plasim.o plasimmod.o specblock.o calmod.o gaussmod.o legmod.o outmod.o miscmod.o fluxmod.o radmod.o surfmod.o landmod.o glaciermod.o seamod.o icemod.o oceanmod.o restartmod.o tracermod.o tpcore.o trc_routines.o aeromod.o aerocore.o pumax_stub.o lsgmod.o cpl_stub.o

toi700d.configure(startemp=3480.0, flux=1167.0, # Stellar parameters ... eccentricity=0.,obliquity=0.,fixedorbit=True, # Orbital parameters ... synchronous=True,rotationperiod=37.426, # Rotation ... radius=1.19,gravity=11.9,aquaplanet=True, # Bulk properties ... pN2=1.47(1-360e-6),pCO2=1.47360e-6,ozone=False, # Atmosphere ... timestep=30.0,snapshots=720,physicsfilter="gp|exp|sp") # Model dynamics Mean Molecular Weight set to 28.0192 g/mol rm: cannot remove ‘/home/users/chasekaa/exomodel/toi700d_run/plasim_restart’: No such file or directory toi700d.exportcfg() Writing configuration.... 1 1167.0 3480.0 None pN2|1.4694707999999999&pCO2|0.0005292000000000001 296.7420501316067 1.4699999999999998 1 0 37.426 1 180.0 None 11.9 1.19 0.0 0.0 None 1 None 1 0 0 gp|exp|sp 8.0 8 15.0 None None None None None None None 50.0 None 0 None None None ECHAM-3 0 None 1 0 None 0 0 None 1.0 50.0 None None 0 None 30.0 None None toggle|0&start|320&end|576&interval|4 720

None 0&2.0&-1.0 0.0005 0.0 None None 0.0 0 1 1.0 0.5 1.0 2.0 0.0 0.0 1.0 0 None 0 5e-09 1 1000.0 1e-12 1 1 None Writing to /home/users/chasekaa/exomodel/toi700d_run/TOI-700d.cfg....

toi700d.run(years=10,crashifbroken=True) Command '['mpiexec -np 4 --use-hwthread-cpus most_plasim_t21_l10_p4.x']' returned non-zero exit status 1. Traceback (most recent call last): File "/home/users/chasekaa/exomodel/exo_env/lib/python3.9/site-packages/exoplasim/init.py", line 1051, in _run subprocess.run([self._exec+self.executable],shell=True,check=True, File "/share/software/user/open/python/3.9.0/lib/python3.9/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['mpiexec -np 4 --use-hwthread-cpus most_plasim_t21_l10_p4.x']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Any and all help figuring this out would be appreciated! Thanks so much.

alphaparrot / ExoPlaSim

exoplasim_tutorial.ipynb failing #33

MPI version: comment this out if you don't have an OpenMPI-enabled compiler (e.g. mpif90)

earth = exo.Model(workdir="earth",modelname="earth",resolution="T21",ncpus=4,layers=10,precision=8)

Single-core version: uncomment if you don't have OpenMPI

Command '['./most_plasim_t21_l10_p1.x']' returned non-zero exit status 127.

MPI version: comment this out if you don't have an OpenMPI-enabled

Single-core version: uncomment if you don't have OpenMPI

clean=False leaves the original output file in place', I am getting the