Apparent installation problem

CADET Troubleshooting
1

Hi everyone,

I’m attempting to build CADET v4.2.0 on a Linux machine (running Ubuntu 20.10). I installed CADET following the directions packaged with the source code (BUILD-LINUX.md), and I didn’t receive any errors (output is given in the attached file). However, when I run cadet-cli with a .h5 file that worked in the previous version of CADET (v4.1.0), I’m receiving ERROR: std::bad_alloc.

For reference, I have installed HDF5 and LAPACK from the Ubuntu repo. I’m using libmkl-dev for LAPACK and BLAS. I did not install SUNDIALS, SuperLU, or UMFPACK since they’re now optional. I have tried building both with and without the -DBLA_VENDOR=Intel10_64lp option.

I’m guessing I made a mistake during installation, but I don’t know how to troubleshoot this. My apologies if I’m missing something that should be obvious. For my future reference, what is the proper way to test if CADET installed correctly?

I sincerely appreciate your help with this!

Thank you,
Chase Herman

install_log.txt (35.8 KB)

2

Hi Chase,

it looks like CADET was compiled correctly. The log you’ve posted seems clean (just a side note: we recommend using MKL in serial mode, i.e., Intel10_64lp_seq).

In order to debug this problem, it would be great if you could provide the .h5 file that triggers this error.

Best,
Sam

3

Hi Sam,

Thank you for your help! Attached is the .h5 file, along with the notebook used to generate it.

Thank you,
Chase

test_case.h5 (34.5 KB)

test_case_no_imports.ipynb (13.8 KB)

4

can confirm the issue.

5

It seems to run on my Windows box (at least in a debug build). Will try it on my Unix box later.

Results from the Windows run:
test_case.h5 (96.9 KB)

6

For me, it also runs in DEBUG mode, but not in RELEASE.

OS: Ubuntu 20.04
cmake version: 3.16.3
gcc version: 9.3.0
7

This hints at a TBB problem: In debug mode, TBB is not used.

8

Thanks to @j.rao and @j.schmoelder, we figured out the following quick fix:
Set NTHREADS to 0 (or a positive number). Do not use a negative number.

Background: NTHREADS is read as int but converted to unsigned int at some point. Since NTHREADS was set to -1, the conversion wrapped around to a ridiculously high (unsigned) number. Apparently, TBB does not care and tries to allocate memory for its jobs based on the number of threads. This resulted in the observed std::bad_alloc.

There’s a fix underway but for now, please use 0 instead of -1.

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9

The fix is provided in commit Fix _nThreads lower bound to 0 (#83) · modsim/CADET@c832f68 · GitHub. Please get the most recent source (https://github.com/modsim/CADET/archive/refs/heads/master.zip) and compile again.

1 Like