Problem installing IBAMR

[Jingwen Xiao]

Hi all,

I have trouble installing IBAMR on a Windows laptop (via WSL) with both autoibamr.sh and building the dependencies manually. When using autoibamr.sh I got:

While installing dependencies manually following https://ibamr.github.io/building, I first encountered an error 

And when I tried to install libmesh again I got the following error even though I'm sure I've installed PETSc (manually, also according to https://ibamr.github.io/building):


Any advice? Thanks!

[Wells, David]

Thanks for reporting this - autoibamr should work on WSL. I think that's the first place to start - it shouldn't be possible for FUNC to not be defined, which implies that something else has done wrong.

Would you please use tee to save the entire console output, i.e., run

./autoibamr.sh --yes 2>&1 | tee all-messages.txt

(on bash and compatible shells so that we capture stdout and stderr) and attach that in an email back to the list?

Best,

David Wells

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From: ibamr...@googlegroups.com <ibamr...@googlegroups.com> on behalf of Jingwen Xiao <xjin...@umich.edu>
Sent: Saturday, December 13, 2025 9:46 AM
To: IBAMR Users <ibamr...@googlegroups.com>
Subject: [ibamr-users] Problem installing IBAMR

 

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[Jingwen Xiao]

Hi David, the log you asked is attached below. 

And since I once cleaned the environment and tried to reinstall PETSc (as before, manually according to https://ibamr.github.io/building), can you also provide some insight on why petscconf.h is missing from my downloaded PETSc package, and where I might be able to find it? Thanks! (I'm aiming for PETSc v3.13.0 or something older but did the same for v3.23.3 to see if changing the version might help, both showed similar problems)

[Wells, David]

Hi,

I don't think I'm capable of answering that PETSc question: if you aren't sure, then try deleting the entire source directory and unpacking it again.

I see that, in H5private.h

#ifdef H5_HAVE_C99_FUNC

#define FUNC __func__

#elif defined(H5_HAVE_FUNCTION)

#define FUNC __FUNCTION__

#else

#error "We need __func__ or __FUNCTION__ to test function names!"

#endif

Here, H5_HAVE_C99_FUNC and H5_HAVE_FUNCTION are defined when the compiler supports those particular special values. There's something about your C compiler which is incompatible with what HDF5 expects - that shouldn't happen in WSL. Do you know what compilers you have installed?

Best,

David Wells

---

From: ibamr...@googlegroups.com <ibamr...@googlegroups.com> on behalf of Jingwen Xiao <xjin...@umich.edu>

Sent: Monday, December 15, 2025 11:05 AM
To: IBAMR Users <ibamr...@googlegroups.com>
Subject: Re: [ibamr-users] Problem installing IBAMR

 

To view this discussion visit https://groups.google.com/d/msgid/ibamr-users/4cd25bfc-b646-446b-bc76-8bd7a4115cd6n%40googlegroups.com.

[Jingwen Xiao]

I'm not sure about that, most installations I've done are based on the IBAMR documentation (I do believe I manually installed libhdf5-openmpi-dev at some point but removed it afterwards). 

Below I attached all the packages I think might be related to the "compilers I installed" by running "apt list '*c*' install",   "apt list 'c*' install",  "apt list 'mpi*' install"  and "apt list '*mpi*' install". 

For further reference, my laptop uses Win11 and currently has nvcc --version V12.0, nvidia-smi CUDA version 13.1/driver version 591.44. 

Hope this helps narrowing down the problem!