h5topng error: invalid colormap file

[Andeloth]

Getting this error when I try to use h5topng

(mp) login04% h5topng -v <filename>              
Using colormap "gray" in file "~/miniconda3/envs/mp/share/h5utils/colormaps/".
h5topng error: invalid colormap file

I just cloned the repo and replaced the old files in the directory with new ones but that didn't fix it.

[linogg]

Hey, I also still get this same problem. Just trying to follow the meep bent-waveguide tutorial line by line but I run into "h5topng errror: invalid colormap file". Tried it on fresh conda-forge installs on differnt machines, both in WSL and on Linux.
Tried the fixes on all other instances of this problem I could find online. Anyone has an idea? Help greatly appreciated :)

[stevengj]

What are the contents of ~/miniconda3/envs/mp/share/h5utils/colormaps/gray? It should be the same as https://github.com/NanoComp/h5utils/blob/master/colormaps/gray

@smartalecH or @mochen4, can you reproduce this?

[Andeloth]

I've experienced this with every colormap I've tried (I tried like 4-5) and they all give the same result. Our research group hasn't been able to use h5topng and other colormap dependent commands for over a year now.

My file matches the one you linked as well.

[linogg]

What are the contents of ~/miniconda3/envs/mp/share/h5utils/colormaps/gray? It should be the same as https://github.com/NanoComp/h5utils/blob/master/colormaps/gray

Yes, its the same. Have also tried different colormaps, same problem.

[stevengj]

Hmm, I suspect that the problem is the tilde in "~/miniconda3/envs/mp/share/h5utils/colormaps/" — ~ is a shell metacharacter, and doesn't generally work in non-shell programs like the fopen function in an arbitrary C program.

I'm not sure what the Conda build is doing to get the tilde into the path? But it might be doing that in an incorrect attempt to try to make the paths relocatable…

The simplest solution might be to update h5topng.c to do tilde expansion: https://stackoverflow.com/questions/15991241/how-do-i-achieve-tilde-expansion-in-c

[stevengj]

Oh, it is probably putting a ~ in the datadir, which we include in the code without doing tilde expansion:

h5utils/configure.ac

Line 235 in e68ec74

AC_DEFINE_UNQUOTED(DATADIR, "$datadir_val", [datadir installation prefix])

[stevengj]

Hopefully should be fixed by bfaac9c, which is in the new 1.13.2 release, once conda updates their binaries.

In the meantime the workaround is to specify the colormap path manually with h5topng -c ~/miniconda3/envs/mp/share/h5utils/colormaps/gray.