problem with quik_tests when install dealii by spack: make -jn test causes to error "bad file descriptor"

[llf m]

Dear all,

I try to install dealii through spack with the illustration in website https://github.com/dealii/dealii/wiki/deal.II-in-Spack, the command is that:

spack install --test=root dealii ^bo...@1.72.0 ^mu...@5.2.0 ^trilinos~exodus~netcdf

The first problem I met is that the installation of the netlib-scalapack through spack would case error:

Error: Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)

8489 | CALL BTRECV(3, 1, NERR2, K, IBTMSGID()+50)
| 2
......
8492 | CALL BTRECV(3, NERR2*6, IERR, K, IBTMSGID()+51)
| 1

Hint by https://github.com/spack/spack/issues/17713, I fix this error by using gcc9 compiler rather than gcc10, which would case the error.

> "This looks like an issue with some of the older Fortran code inside netlib-scalapack relying on unspecified/non-standards-compliant behavior, probably triggered by a change in default with GCC 10 (which you're using) compared to older versions. GCC10 is pretty new."

The second problem is that installing trilinos would case error:

stray '\' in program

this error also cause by a incompatible behavior which cause by make4.3, after using an old version of make, the error disappeared.

And the third problem is that in spack build phase of dealii cause an error:

==> Error: ProcessError: Command exited with status 2:
   'make' '-j8' 'test'

5356          Start  1: step.debug
    5357     1/23 Test  #1: step.debug .......................***Failed   
              0.12 sec
    5358    make[6]: *** read jobs pipe: Bad file descriptor.  Stop.
    5359    make[6]: *** Waiting for unfinished jobs....
 >> 5360    make[5]: *** [CMakeFiles/Makefile2:8062: tests/quick_tests/CM
            akeFiles/step.debug.run.dir/rule] Error 2

This error happened in build of the quick_tests, even though I have set the OMP_NUM_THREADS=1 which suggested by issue:

https://github.com/dealii/dealii/issues/6589

https://github.com/dealii/dealii/pull/7143

and the old mail in dealii mailing list.

Then I go to the dealii quick_tests directory of spack-build, if I use "make test" then everything is right, but if use "make -j8(n) test" then the error appears again. 

The spack command I used is

spack install --test=root dealii%g...@9.3.0 ^boost@1.72.0 ^mu...@5.2.0 ^trilinos%g...@9.3.0~exodus~netcdf

the compiler is gcc9.3.0 and make version is 4.2.1. The spack build log and env are attached. And the log of quick_tests by manually build ("make -j8 test") is also attached. Any suggection would be appreciated.

Thanks,

m.

[Bruno Turcksin]

It looks like I clicked on the wrong button and I didn't sent the message to the mailing list :( There are two solutions to this problem:

1. Compile everything using a single processor, i.e. using spack install -j1 ... This works but it will be very slow

2. Do not run quicktest when using spack. This can be done by omitting --test=root.

Bruno

[llf m]

Thank you for your help. Exactly, it can be solved simply by your solution. Someone might want to install dealii by spack would also need the some suggestion and would meet these problems repeatly, and hope this mail can be helpful. Also if the dealii website that about the spack can mention these troubleshootings might be helpful.

thanks,

m.

Bruno Turcksin <bruno.t...@gmail.com> 于 2021年6月18日周五 下午9:22写道：

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[llf m]

sorry, I have seen the bottom of page said that incompatible with cmake version greater 3.10. But the netlib-scalapck incompatible with gcc10 and trilinos incompatible with make4.3 may also cause troubles.

llf m <miff...@gmail.com> 于 2021年6月19日周六 上午12:37写道：