To install CLAWPACK (version mentioned below) properly, I ran Arch Linux and followed the pip installation, using the Fortran compiler Gfortran, and Jupyter notebook for interfacing with code. The username for the machine in this guide is jack, so replace this with the username with your machine where necessary. vim is used as the text editor in this guide, so replace it with your preferred editor. If you are running a different terminal to bash, replace ~/.bashrc with your shell's alternative (e.g ~/.zshrc) for a zsh-based terminal.
Even if you are not running the same OS as in this guide, or running an alternative to another program mentioned here, this guide should point you in the right direction for fixes to be made on your device, you will just need to find out how to 'translate' these instructions to the service you are working with.
export CLAW_VERSION=v5.7.0 #The CLAWPACK version this notebook runs on
After running the pip install command at:
https://www.clawpack.org/installing.html#pip-install
This is the code block at which we need to adapt the instructions:
export CLAW=$HOME/clawpack_src/clawpack-$CLAW_VERSION
export FC=gfortran
Example where it occurs (post installation) :
At first cell under the section Compile and run the GeoClaw code, with contents:
nbtools.make_exe(new=True, verbose=True) # compile xgeoclaw
These commands set the environmental variables CLAW and FC temporarily. Upon restart, they will no longer exist.
Example where it occurs (post installation) :
When running cell, output is :
Executing shell command: make new
*** Possible errors, return_code = 2
Done... Check this file to see output:
compile_output.txt
In the compile_output.txt file, at the bottom, it reads :
Makefile:57: /clawutil/src/Makefile.common: No such file or directory
make: *** No rule to make target '/clawutil/src/Makefile.common'. Stop.
Indeed, on the linux machine /clawutil/src/Makefile.common is not a valid location (considering the first / is the root of the filesystem).
For the following, replace vim with your editor of choice. If you are running a different terminal to bash, replace ~/.bashrc with your shell's alternative (e.g ~/.zshrc) for a zsh-based terminal.
The commands must be inserted into configuration files to become permanent. Enter the following into a terminal:
sudo vim ~/.profile
Insert these commands at the end of the file :
export CLAW=$HOME/clawpack_src/clawpack-$CLAW_VERSION
export FC=gfortran
Save and exit the editor (vim).
sudo vim ~/.bashrc
Insert these commands at the end of the file :
export CLAW=$HOME/clawpack_src/clawpack-$CLAW_VERSION
export FC=gfortran
Save and exit the editor (vim).
Now restart your machine, and test if these work.
You can test whether you have set the environmental variables using running (in the command line):
printenv CLAW FC
Which if successful will output:
/home/jack/clawpack_src/clawpack-$CLAW_VERSION
gfortran
Rerunning the cell from the example, the output should now read :
Executing shell command: make new
Done... Check this file to see output:
compile_output.txt
If you don't get this, see the other problem entries for troubleshooting
$ jupyter notebook
This error should occur for any CLAWPACK simulation that requires the library clawutils (which is probably all of them), but this is the location of an example where it occurs:
At first cell under the section Compile and run the GeoClaw code, with contents:
nbtools.make_exe(new=True, verbose=True) # compile xgeoclaw
When running cell, output is :
Executing shell command: make new
*** Possible errors, return_code = 2
Done... Check this file to see output:
compile_output.txt
In the compile_output.txt file, at the bottom, it reads :
/home/jack/clawpack_src/clawpack-$CLAW_VERSION/geoclaw/src/2d/shallow/filval.f90:154:51:
95 | call preintcopy(valc,mic,mjc,nvar,iclo,ichi,jclo,jchi,level-1,fliparray)
| 2
......
154 | jlo-nghost,jhi+nghost,level,1,1,fliparray)
| 1
Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/REAL(8)).
make: *** [/home/jack/clawpack_src/clawpack-$CLAW_VERSION/clawutil/src/Makefile.common:130: /home/jack/clawpack_src/clawpack-v5.7.0/geoclaw/src/2d/shallow/filval.o] Error 1
make: *** [/home/jack/clawpack_src/clawpack-$CLAW_VERSION/clawutil/src/Makefile.common:274: new] Error 2
We can trace the error back to the file in the first line in this code block, which is a fortran 90 file.
Find the Makefile you call when building the simulation (usually in the same folder as the notebook used to execute the simulation). In this example, it was located at :
Around line 24, where it says
# Compiler flags can be specified here or set as an environment variable
FFLAGS ?=
The following should be used:
FFLAGS ?= -fallow-argument-mismatch
I think this error is related to a gfortran 10, as a github user in the gfortran repository reported an issue on the same 'Error: Type mismatch' on a .f90 file when changing from gfortran 9 to 10.
Rerunning the cell from the example, the output should now read :
Executing shell command: make new
Done... Check this file to see output:
compile_output.txt
If you don't get this, see the other problem entries for troubleshooting