Segmentation fault invalid memory reference #1270

vanchisen · 2024-05-07T02:40:53Z

vanchisen
May 7, 2024

Dear Neko developers and users,
Thank you for great job that makes NekO public available.
I built neko-0.7.2 on my local workstation with 8 RTX 4090 GPUs.
The building process was smooth, however when I try to run the simulation, it gives me segmentation errors posted below.
Any hints about the error ?

_  __  ____  __ __  ____

/ |/ / / / / /// / __
/ / / / / ,< / // /
//|/ // //|| ____/

(version: 0.7.2)
(build: 2024-05-07 on x86_64-pc-linux-gnu using gnu)

-------Job Information--------
Start time: 06:46 / 2024-05-07
Running on: 2 MPI ranks
CPU type : Intel(R) Xeon(R) Gold 6226R CPU @ 2.90GHz
Bcknd type: Accelerator (CUDA)
Dev. name : NVIDIA GeForce RTX 4090
Real type : double precision

-------------Case-------------
Reading case file pipe.case

-------------Mesh-------------
Reading a binary Neko file pipe.nmsh
gdim = 3, nelements = 36480
Reading elements
Reading BC/zone data
Reading deformation data
Mesh read, setting up connectivity
Done setting up mesh and connectivity

-----Material properties------
Read non-dimensional values:
Re : 2.650000E+03
Set dimensional values:
rho : 1.000000E+00
mu : 3.773585E-04

  ------------Fluid-------------  
  Type       : Modular (Pn/Pn)
  lx         : 6
  rho        : 1.000000E+00
  mu         : 3.773585E-04
  Ksp vel.   : (cg, jacobi)
   `-abs tol : 1.000000E-07
  Ksp prs.   : (gmres, hsmg)
   `-abs tol : 1.000000E-04
  Dealias    : T
  Save bdry  : T

      --------Gather-Scatter--------  
      Comm         :   Device MPI
      Avg. internal:      2707560
      Avg. external:        28440
      Backend      :         cuda

[wzc-X11DPG-OT:472013] Read -1, expected 159976, errno = 14
[wzc-X11DPG-OT:472012] Read -1, expected 159976, errno = 14

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x73ee96823960 in ???
#1 0x73ee96822ac5 in ???
#2 0x73ee9644251f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#0 0x79fbf5c23960 in ???
#1 0x79fbf5c22ac5 in ???
#2 0x79fbf584251f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x73ee965aedcd in ???
at ../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S:317
#4 0x73ee8b936243 in ???
#5 0x73ee8b85f555 in ???
#6 0x73ee8b85d810 in ???
#7 0x73ee8b93aae4 in ???
#8 0x73ee8b93af90 in ???
#3 0x79fbf59aedcd in ???
at ../sysdeps/x86_64/multiarch/memmove-vec-unaligned-erms.S:317
#4 0x79fbeae24243 in ???
#5 0x79fbea847555 in ???
#6 0x79fbea845810 in ???
#7 0x79fbeae28ae4 in ???
#8 0x79fbeae28f90 in ???
#9 0x73ee96376713 in ???
#10 0x73ee9932f744 in ???
#9 0x79fbf5ab9713 in ???
#10 0x79fbf60c9744 in ???
#11 0x79fbf610a326 in ???
#11 0x73ee99370326 in ???
#12 0x6106d1e6ba06 in __gs_device_mpi_MOD_gs_device_mpi_nbwait
at gs/bcknd/device/gs_device_mpi.F90:424
#12 0x5ac32c9cea06 in __gs_device_mpi_MOD_gs_device_mpi_nbwait
at gs/bcknd/device/gs_device_mpi.F90:424
#13 0x6106d1e6dceb in __gather_scatter_MOD_gs_op_vector
at gs/gather_scatter.f90:1313
#14 0x6106d1e784fc in __gather_scatter_MOD_gs_init
at gs/gather_scatter.f90:209
#13 0x5ac32c9d0ceb in __gather_scatter_MOD_gs_op_vector
at gs/gather_scatter.f90:1313
#14 0x5ac32c9db4fc in __gather_scatter_MOD_gs_init
at gs/gather_scatter.f90:209
#15 0x6106d1f59920 in __fluid_scheme_MOD_fluid_scheme_init_common
at fluid/fluid_scheme.f90:305
#16 0x6106d1f5b406 in __fluid_scheme_MOD_fluid_scheme_init_all
at fluid/fluid_scheme.f90:528
#15 0x5ac32cabc920 in __fluid_scheme_MOD_fluid_scheme_init_common
at fluid/fluid_scheme.f90:305
#16 0x5ac32cabe406 in __fluid_scheme_MOD_fluid_scheme_init_all
at fluid/fluid_scheme.f90:528
#17 0x5ac32cad4564 in __fluid_pnpn_MOD_fluid_pnpn_init
at fluid/fluid_pnpn.f90:132
#17 0x6106d1f71564 in __fluid_pnpn_MOD_fluid_pnpn_init
at fluid/fluid_pnpn.f90:132
#18 0x6106d1f53d9b in case_init_common
at /home/wzc/neko-0.7.2/src/case.f90:206
#19 0x6106d1f567f6 in __case_MOD_case_init_from_file
#18 0x5ac32cab6d9b in case_init_common
at /home/wzc/neko-0.7.2/src/case.f90:206
#19 0x5ac32cab97f6 in __case_MOD_case_init_from_file
at /home/wzc/neko-0.7.2/src/case.f90:117
at /home/wzc/neko-0.7.2/src/case.f90:117
#20 0x5ac32cb212a6 in __neko_MOD_neko_init
at /home/wzc/neko-0.7.2/src/neko.f90:255
#20 0x6106d1fbe2a6 in __neko_MOD_neko_init
at /home/wzc/neko-0.7.2/src/neko.f90:255
#21 0x5ac32cb845e9 in turboneko
at /home/wzc/neko-0.7.2/src/driver.f90:6
#22 0x5ac32c999e2e in main
at /home/wzc/neko-0.7.2/src/driver.f90:3
#21 0x6106d20215e9 in turboneko
at /home/wzc/neko-0.7.2/src/driver.f90:6
#22 0x6106d1e36e2e in main
at /home/wzc/neko-0.7.2/src/driver.f90:3

Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.

mpirun noticed that process rank 0 with PID 0 on node wzc-X11DPG-OT exited on signal 11 (Segmentation fault).

Best Wishes,
Zhicheng Wang

njansson · 2024-05-07T09:04:30Z

njansson
May 7, 2024
Maintainer

I would suggest to start looking at your MPI installation, and make sure that it supports GPU aware MPI. One often gets these segmentation faults if Neko is configured with device MPI, and the MPI installation doesn't support it.

0 replies

vanchisen · 2024-05-07T14:11:02Z

vanchisen
May 7, 2024
Author

Thank you very much Niclas Jansson.
so mpirun --version tells me I'm using Open MPI 4.1.2.
I think it supports CUDA. OMPI's website indicates they support CUDA since version 1.7.2,

1 reply

adperezm May 7, 2024
Collaborator

Hi,

May I ask two things?

How are you configuring neko? i.e., can you show the command you use?
I see that you run in 2 ranks and you mentioned you had 8 GPUs in your workstation. Could you show the command you use to execute neko?

I do not know the reason for the segfault, but I just want to know your configuration to try to get ideas.

vanchisen · 2024-05-07T14:52:52Z

vanchisen
May 7, 2024
Author

Thank you.
The following are the command of compiling running neko,

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
cmake -DCMAKE_INSTALL_REFIX=/home/wzc/json-fortran-8.4.0/installation -DUSE_GNU_INSTALL_CONVENTION=ON ../
sudo make install

export PKG_CONFIG_PATH=/home/wzc/json-fortran-8.4.0/installation/lib/pkgconfig:$PKG_CONFIG_PATH
export LD_LIBRARY_PATH=/home/wzc/json-fortran-8.4.0/installation/lib:$LD_LIBRARY_PATH

cd gslib-master
make

export GSLIB=/home/wzc/gslib-master/build

tar xvf parmetis-4.0.3.tar
cd parmetis-4.0.3.tar
make config prefix=/home/wzc/parmetis-4.0.3/installation
make install

cd neko-0.7.2

./configure FC=gfortran CC=gcc
MPIFC=mpif90 MPICC=mpicc
FCGLAGS="-02 -pedantic -std=f2008"
--prefix=/home/wzc/neko-7.2/installation
--with-gslib=/home/wzc/gslib-master/build
--with-parmetis=/home/wzc/parmetis-4.0.3/installation
--enable-contrib
--enable-device-mpi
--with-cuda=/usr/local/cuda CUDA_FLAGS=-03 CUDA_ARCH=-arch=sm_80 NVCC=/usr/local/cuda/bin/nvcc

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH

export CUDA_VISIBLE_DEVICES=0,1,2,3,5,6,7

mpirun --allow-run-as-root -np 4 ./neko pipe.case >& out &

1 reply

adperezm May 7, 2024
Collaborator

Okay thanks!

Just to check Niclas initially said, I would recomend: remove the "--enable-device-mpi" from the configuration and then try to run again. Here we would see if maybe it comes from the MPI implementation as previously conjectured.

Regarding running with multiple devices, I think that you will need to run with as many mpi ranks as you have devices. @njansson can confirm.

njansson · 2024-05-07T15:29:14Z

njansson
May 7, 2024
Maintainer

Thank you very much Niclas Jansson.

so mpirun --version tells me I'm using Open MPI 4.1.2.

I think it supports CUDA. OMPI's website indicates they support CUDA since version 1.7.2,

Yes openmpi supports it, but it needs to be specifically configured for cuda when installed

0 replies

vanchisen · 2024-05-07T15:32:56Z

vanchisen
May 7, 2024
Author

Thank you Adperezm and Niclas.
After removing --enable-device-mpi, re-configure and re-compile, I still get same error.
Below I attached the whole configure log, in case it can give any help,

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
his file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by neko configure 0.7.2, which was
generated by GNU Autoconf 2.69. Invocation command line was

$ ./configure FC=gfortran CC=gcc MPIFC=mpif90 MPICC=mpicc FCGLAGS=-02 -pedantic -std=f2008 --prefix=/home/wzc/neko-0.7.2/installation --with-gslib=/home/wzc/gslib-master/build --with-parmetis=/home/wzc/parmetis-4.0.3/installation --enable-contrib --with-cuda=/usr/local/cuda CUDA_FLAGS=-03 CUDA_ARCH=-arch=sm_80 NVCC=/usr/local/cuda/bin/nvcc

---------

Platform.

---------

hostname = wzc-X11DPG-OT
uname -m = x86_64
uname -r = 6.5.0-28-generic
uname -s = Linux
uname -v = #29~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Apr 4 14:39:20 UTC 2

/usr/bin/uname -p = x86_64
/bin/uname -X = unknown

/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown

PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /usr/games
PATH: /usr/local/games
PATH: /snap/bin
PATH: /snap/bin

-----------

Core tests.

-----------

configure:2646: checking for a BSD-compatible install
configure:2714: result: /usr/bin/install -c
configure:2725: checking whether build environment is sane
configure:2780: result: yes
configure:2931: checking for a thread-safe mkdir -p
configure:2970: result: /usr/bin/mkdir -p
configure:2977: checking for gawk
configure:3007: result: no
configure:2977: checking for mawk
configure:2993: found /usr/bin/mawk
configure:3004: result: mawk
configure:3015: checking whether make sets $(MAKE)
configure:3037: result: yes
configure:3066: checking whether make supports nested variables
configure:3083: result: yes
configure:3210: checking whether to enable maintainer-specific portions of Makefiles
configure:3219: result: no
configure:3237: checking build system type
configure:3251: result: x86_64-pc-linux-gnu
configure:3271: checking host system type
configure:3284: result: x86_64-pc-linux-gnu
configure:3352: checking for ranlib
configure:3368: found /usr/bin/ranlib
configure:3379: result: ranlib
configure:3547: checking for Fortran compiler version
configure:3556: gfortran --version >&5
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:3567: $? = 0
configure:3556: gfortran -v >&5
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu122.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu122.04)
... rest of stderr output deleted ...
configure:3567: $? = 0
configure:3556: gfortran -V >&5
gfortran: error: unrecognized command-line option '-V'
gfortran: fatal error: no input files
compilation terminated.
configure:3567: $? = 1
configure:3556: gfortran -qversion >&5
gfortran: error: unrecognized command-line option '-qversion'; did you mean '--version'?
gfortran: fatal error: no input files
compilation terminated.
configure:3567: $? = 1
configure:3582: checking whether the Fortran compiler works
configure:3604: gfortran conftest.f >&5
configure:3608: $? = 0
configure:3656: result: yes
configure:3659: checking for Fortran compiler default output file name
configure:3661: result: a.out
configure:3667: checking for suffix of executables
configure:3674: gfortran -o conftest conftest.f >&5
configure:3678: $? = 0
configure:3700: result:
configure:3716: checking whether we are cross compiling
configure:3724: gfortran -o conftest conftest.f >&5
configure:3728: $? = 0
configure:3735: ./conftest
configure:3739: $? = 0
configure:3754: result: no
configure:3759: checking for suffix of object files
configure:3775: gfortran -c conftest.f >&5
configure:3779: $? = 0
configure:3800: result: o
configure:3808: checking whether we are using the GNU Fortran compiler
configure:3821: gfortran -c conftest.F >&5
configure:3821: $? = 0
configure:3830: result: yes
configure:3836: checking whether gfortran accepts -g
configure:3847: gfortran -c -g conftest.f >&5
configure:3847: $? = 0
configure:3855: result: yes
configure:3893: checking for coarray support
configure:3905: gfortran -c -g -O2 conftest.f >&5
conftest.f:3:21:

3 |        integer :: i[*]
  |                     1

Fatal Error: Coarrays disabled at (1), use '-fcoarray=' to enable
compilation terminated.
configure:3905: $? = 1
configure: failed program was:
|
| program conftest
| integer :: i[]
| integer :: image_num
| image_num = this_image()
| sync all
| sync images()
| end program conftest
configure:3925: result: no
configure:3939: checking for derived type I/O support
configure:3968: gfortran -c -g -O2 conftest.f >&5
configure:3968: $? = 0
configure:3982: result: yes
configure:4003: checking for REAL128 support
configure:4018: gfortran -c -g -O2 conftest.f >&5
configure:4018: $? = 0
configure:4032: result: yes
configure:4054: checking for mpif90
configure:4081: result: mpif90
configure:4099: checking for MPI_Init
configure:4106: mpif90 -o conftest -g -O2 conftest.f >&5
configure:4106: $? = 0
configure:4108: result: yes
configure:4237: checking for mpif.h
configure:4244: mpif90 -c -g -O2 conftest.f >&5
configure:4244: $? = 0
configure:4245: result: yes
configure:4289: checking for style of include used by make
configure:4317: result: GNU
configure:4388: checking for gcc
configure:4415: result: gcc
configure:4644: checking for C compiler version
configure:4653: gcc --version >&5
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:4664: $? = 0
configure:4653: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu122.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu122.04)
... rest of stderr output deleted ...
configure:4664: $? = 0
configure:4653: gcc -V >&5
gcc: error: unrecognized command-line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:4664: $? = 1
configure:4653: gcc -qversion >&5
gcc: error: unrecognized command-line option '-qversion'; did you mean '--version'?
gcc: fatal error: no input files
compilation terminated.
configure:4664: $? = 1
configure:4668: checking whether we are using the GNU C compiler
configure:4687: gcc -c conftest.c >&5
configure:4687: $? = 0
configure:4696: result: yes
configure:4705: checking whether gcc accepts -g
configure:4725: gcc -c -g conftest.c >&5
configure:4725: $? = 0
configure:4766: result: yes
configure:4783: checking for gcc option to accept ISO C89
configure:4846: gcc -c -g -O2 conftest.c >&5
configure:4846: $? = 0
configure:4859: result: none needed
configure:4884: checking whether gcc understands -c and -o together
configure:4906: gcc -c conftest.c -o conftest2.o
configure:4909: $? = 0
configure:4906: gcc -c conftest.c -o conftest2.o
configure:4909: $? = 0
configure:4921: result: yes
configure:4940: checking dependency style of gcc
configure:5051: result: gcc3
configure:5076: checking for mpicc
configure:5103: result: mpicc
configure:5214: checking for mpi.h
configure:5227: mpicc -c -g -O2 conftest.c >&5
configure:5227: $? = 0
configure:5228: result: yes
configure:5320: checking for g++
configure:5336: found /usr/bin/g++
configure:5347: result: g++
configure:5374: checking for C++ compiler version
configure:5383: g++ --version >&5
g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:5394: $? = 0
configure:5383: g++ -v >&5
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/11/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu122.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-11-XeT9lY/gcc-11-11.4.0/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu122.04)
... rest of stderr output deleted ...
configure:5394: $? = 0
configure:5383: g++ -V >&5
g++: error: unrecognized command-line option '-V'
g++: fatal error: no input files
compilation terminated.
configure:5394: $? = 1
configure:5383: g++ -qversion >&5
g++: error: unrecognized command-line option '-qversion'; did you mean '--version'?
g++: fatal error: no input files
compilation terminated.
configure:5394: $? = 1
configure:5398: checking whether we are using the GNU C++ compiler
configure:5417: g++ -c conftest.cpp >&5
configure:5417: $? = 0
configure:5426: result: yes
configure:5435: checking whether g++ accepts -g
configure:5455: g++ -c -g conftest.cpp >&5
configure:5455: $? = 0
configure:5496: result: yes
configure:5521: checking dependency style of g++
configure:5632: result: gcc3
configure:5657: checking for mpic++
configure:5673: found /usr/bin/mpic++
configure:5684: result: mpic++
configure:5795: checking for mpi.h
configure:5808: mpic++ -c -g -O2 conftest.cpp >&5
configure:5808: $? = 0
configure:5809: result: yes
configure:5852: checking for Fortran 2008 MPI support
configure:5860: mpif90 -c -g -O2 conftest.f >&5
configure:5860: $? = 0
configure:5874: result: yes
configure:5895: checking if MPI datatypes can be parameters
configure:5904: mpif90 -c -g -O2 conftest.f >&5
configure:5904: $? = 0
configure:5918: result: yes
configure:5934: checking for Fortran flag to compile preprocessed .F90 files
configure:5959: mpif90 -c -g -O2 conftest.F90 >&5
configure:5959: $? = 0
configure:5969: mpif90 -c -g -O2 conftest.F90 >&5
conftest.F90:5:2:

5 |       choke me
  |  1    ~~~~~~~~

Fatal Error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:5969: $? = 1
configure: failed program was:
| program main
|
| #if 1
| #include <ac_nonexistent.h>
| choke me
| #endif
| end
configure:5982: result: none
configure:6003: checking for Fortran compiler vendor
configure:6056: mpif90 -c -g -O2 conftest.F90 >&5
conftest.F90:4:7:

4 |       thisisanerror;
  |       1

Error: Unclassifiable statement at (1)
configure:6056: $? = 1
configure: failed program was:
| program main
|
| #if !(defined(__ICC) || defined(__ECC) || defined(__INTEL_COMPILER))
| thisisanerror;
| #endif
|
| end
configure:6056: mpif90 -c -g -O2 conftest.F90 >&5
conftest.F90:4:7:

4 |       thisisanerror;
  |       1

Error: Unclassifiable statement at (1)
configure:6056: $? = 1
configure: failed program was:
| program main
|
| #if !(defined(xlc) || defined(xlC) || defined(IBMC) || defined(IBMCPP) || defined(ibmxl))
| thisisanerror;
| #endif
|
| end
configure:6056: mpif90 -c -g -O2 conftest.F90 >&5
conftest.F90:4:7:

4 |       thisisanerror;
  |       1

Error: Unclassifiable statement at (1)
configure:6056: $? = 1
configure: failed program was:
| program main
|
| #if !(defined(PATHCC) || defined(PATHSCALE))
| thisisanerror;
| #endif
|
| end
configure:6056: mpif90 -c -g -O2 conftest.F90 >&5
conftest.F90:4:7:

4 |       thisisanerror;
  |       1

4 |       thisisanerror;
  |       1

Error: Unclassifiable statement at (1)
configure:6056: $? = 1
configure: failed program was:
| program main
|
| #if !(defined(_CRAYC) || defined(_CRAYFTN))
| thisisanerror;
| #endif
|
| end
configure:6056: mpif90 -c -g -O2 conftest.F90 >&5
conftest.F90:4:7:

4 |       thisisanerror;
  |       1

4 |       thisisanerror;
  |       1

Error: Unclassifiable statement at (1)
configure:6056: $? = 1
configure: failed program was:
| program main
|
| #if !(defined(SDCC) || defined(__SDCC))
| thisisanerror;
| #endif
|
| end
configure:6056: mpif90 -c -g -O2 conftest.F90 >&5
conftest.F90:4:7:

4 |       thisisanerror;
  |       1

4 |       thisisanerror;
  |       1

4 |       thisisanerror;
  |       1

Error: Unclassifiable statement at (1)
configure:6056: $? = 1
configure: failed program was:
| program main
|
| #if !(defined(_PGI))
| thisisanerror;
| #endif
|
| end
configure:6056: mpif90 -c -g -O2 conftest.F90 >&5
configure:6056: $? = 0
configure:6065: result: gnu
configure:6083: checking how to run the C preprocessor
configure:6114: mpicc -E conftest.c
configure:6114: $? = 0
configure:6128: mpicc -E conftest.c
conftest.c:15:10: fatal error: ac_nonexistent.h: No such file or directory
15 | #include <ac_nonexistent.h>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:6128: $? = 1
configure: failed program was:
| /* confdefs.h /
| #define PACKAGE_NAME "neko"
| #define PACKAGE_TARNAME "neko"
| #define PACKAGE_VERSION "0.7.2"
| #define PACKAGE_STRING "neko 0.7.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "neko"
| #define VERSION "0.7.2"
| #define HAVE_DERIVED_TYPE_IO 1
| #define HAVE_REAL128 1
| #define HAVE_MPI_F08 1
| #define HAVE_MPI_PARAM_DTYPE 1
| / end confdefs.h. /
| #include <ac_nonexistent.h>
configure:6153: result: mpicc -E
configure:6173: mpicc -E conftest.c
configure:6173: $? = 0
configure:6187: mpicc -E conftest.c
conftest.c:15:10: fatal error: ac_nonexistent.h: No such file or directory
15 | #include <ac_nonexistent.h>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
configure:6187: $? = 1
configure: failed program was:
| / confdefs.h /
| #define PACKAGE_NAME "neko"
| #define PACKAGE_TARNAME "neko"
| #define PACKAGE_VERSION "0.7.2"
| #define PACKAGE_STRING "neko 0.7.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "neko"
| #define VERSION "0.7.2"
| #define HAVE_DERIVED_TYPE_IO 1
| #define HAVE_REAL128 1
| #define HAVE_MPI_F08 1
| #define HAVE_MPI_PARAM_DTYPE 1
| / end confdefs.h. */
| #include <ac_nonexistent.h>
configure:6216: checking for grep that handles long lines and -e
configure:6274: result: /usr/bin/grep
configure:6279: checking for egrep
configure:6341: result: /usr/bin/grep -E
configure:6346: checking for ANSI C header files
configure:6366: mpicc -c -g -O2 conftest.c >&5
configure:6366: $? = 0
configure:6439: mpicc -o conftest -g -O2 conftest.c >&5
configure:6439: $? = 0
configure:6439: ./conftest
configure:6439: $? = 0
configure:6450: result: yes
configure:6463: checking for sys/types.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6463: checking for sys/stat.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6463: checking for stdlib.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6463: checking for string.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6463: checking for memory.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6463: checking for strings.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6463: checking for inttypes.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6463: checking for stdint.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6463: checking for unistd.h
configure:6463: mpicc -c -g -O2 conftest.c >&5
configure:6463: $? = 0
configure:6463: result: yes
configure:6477: checking cpuid.h usability
configure:6477: mpicc -c -g -O2 conftest.c >&5
configure:6477: $? = 0
configure:6477: result: yes
configure:6477: checking cpuid.h presence
configure:6477: mpicc -E conftest.c
configure:6477: $? = 0
configure:6477: result: yes
configure:6477: checking for cpuid.h
configure:6477: result: yes
configure:6507: checking for doxygen
configure:6537: result: no
configure:6603: checking for makedepf90
configure:6633: result: no
configure:6655: checking for flint
configure:6685: result: no
configure:6704: checking for a Cray XT, XE, XC system
configure:6726: result: no
configure:6738: checking for a HPE Cray system
configure:6760: result: no
configure:6784: checking for a NEC SX-Aurora system
conftest.c:26:20: error: missing '(' in expression
26 | #if defined(ve))
| ^
configure:6806: result: no
configure:6841: checking for pFUnit
configure:6844: result: no
configure:6942: checking if sgemm is being linked in already
configure:6949: mpif90 -o conftest -g -O2 conftest.F90 >&5
/usr/bin/ld: /tmp/ccopUoRm.o: in function main': /home/wzc/neko-0.7.2/conftest.F90:2: undefined reference to sgemm'
collect2: error: ld returned 1 exit status
configure:6949: $? = 1
configure: failed program was:
| program main
| call sgemm
| end
configure:6954: result: no
configure:6961: checking for sgemm in -lopenblas
configure:6973: mpif90 -o conftest -g -O2 conftest.F90 -lopenblas >&5
configure:6973: $? = 0
configure:6982: result: yes
configure:7740: checking for cheev
configure:7740: mpif90 -o conftest -g -O2 conftest.F90 -lopenblas >&5
configure:7740: $? = 0
configure:7740: result: yes
configure:8133: checking parmetis.h usability
configure:8133: mpicc -c -g -O2 -I/home/wzc/parmetis-4.0.3/installation/include conftest.c >&5
In file included from conftest.c:61:
/home/wzc/parmetis-4.0.3/installation/include/parmetis.h:18:10: fatal error: metis.h: No such file or directory
18 | #include <metis.h>
| ^~~~~~~~~
compilation terminated.
configure:8133: $? = 1
configure: failed program was:
| /* confdefs.h /
| #define PACKAGE_NAME "neko"
| #define PACKAGE_TARNAME "neko"
| #define PACKAGE_VERSION "0.7.2"
| #define PACKAGE_STRING "neko 0.7.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "neko"
| #define VERSION "0.7.2"
| #define HAVE_DERIVED_TYPE_IO 1
| #define HAVE_REAL128 1
| #define HAVE_MPI_F08 1
| #define HAVE_MPI_PARAM_DTYPE 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_CPUID_H 1
| #define HAVE_BLAS 1
| #define HAVE_LAPACK 1
| / end confdefs.h. /
| #include <stdio.h>
| #ifdef HAVE_SYS_TYPES_H
| # include <sys/types.h>
| #endif
| #ifdef HAVE_SYS_STAT_H
| # include <sys/stat.h>
| #endif
| #ifdef STDC_HEADERS
| # include <stdlib.h>
| # include <stddef.h>
| #else
| # ifdef HAVE_STDLIB_H
| # include <stdlib.h>
| # endif
| #endif
| #ifdef HAVE_STRING_H
| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
| # include <memory.h>
| # endif
| # include <string.h>
| #endif
| #ifdef HAVE_STRINGS_H
| # include <strings.h>
| #endif
| #ifdef HAVE_INTTYPES_H
| # include <inttypes.h>
| #endif
| #ifdef HAVE_STDINT_H
| # include <stdint.h>
| #endif
| #ifdef HAVE_UNISTD_H
| # include <unistd.h>
| #endif
| #include <parmetis.h>
configure:8133: result: no
configure:8133: checking parmetis.h presence
configure:8133: mpicc -E -I/home/wzc/parmetis-4.0.3/installation/include conftest.c
In file included from conftest.c:28:
/home/wzc/parmetis-4.0.3/installation/include/parmetis.h:18:10: fatal error: metis.h: No such file or directory
18 | #include <metis.h>
| ^~~~~~~~~
compilation terminated.
configure:8133: $? = 1
configure: failed program was:
| / confdefs.h /
| #define PACKAGE_NAME "neko"
| #define PACKAGE_TARNAME "neko"
| #define PACKAGE_VERSION "0.7.2"
| #define PACKAGE_STRING "neko 0.7.2"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| #define PACKAGE "neko"
| #define VERSION "0.7.2"
| #define HAVE_DERIVED_TYPE_IO 1
| #define HAVE_REAL128 1
| #define HAVE_MPI_F08 1
| #define HAVE_MPI_PARAM_DTYPE 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_CPUID_H 1
| #define HAVE_BLAS 1
| #define HAVE_LAPACK 1
| / end confdefs.h. */
| #include <parmetis.h>
configure:8133: result: no
configure:8133: checking for parmetis.h
configure:8133: result: no
configure:8152: checking for ParMETIS_V3_PartMeshKway in -lparmetis
configure:8164: mpif90 -o conftest -g -O2 -L/home/wzc/parmetis-4.0.3/installation/lib conftest.F90 -lparmetis -lmetis -lopenblas >&5
/usr/bin/ld: cannot find -lmetis: No such file or directory
collect2: error: ld returned 1 exit status
configure:8164: $? = 1
configure: failed program was:
| program main
| call ParMETIS_V3_PartMeshKway
| end
configure:8173: result: no
configure:8375: checking for fgslib_gs_setup in -lgs
configure:8387: mpif90 -o conftest -g -O2 -L/home/wzc/gslib-master/build/lib -L/home/wzc/gslib-master/build conftest.F90 -lgs >&5
configure:8387: $? = 0
configure:8396: result: yes
configure:8517: checking for pkg-config
configure:8535: found /usr/bin/pkg-config
configure:8547: result: /usr/bin/pkg-config
configure:8572: checking pkg-config is at least version 0.9.0
configure:8575: result: yes
configure:9022: checking for nvcc
configure:9053: result: /usr/local/cuda/bin/nvcc
configure:9082: checking for cudaFree in -lcudart
configure:9107: /usr/local/cuda/bin/nvcc -o conftest -L/usr/local/cuda/lib64 conftest.c -lcudart >&5
configure:9107: $? = 0
configure:9116: result: yes
configure:9733: checking for json-fortran >= 7.1.0
configure:9740: $PKG_CONFIG --exists --print-errors "json-fortran >= 7.1.0"
configure:9743: $? = 0
configure:9757: $PKG_CONFIG --exists --print-errors "json-fortran >= 7.1.0"
configure:9760: $? = 0
configure:9818: result: yes
configure:10034: checking that generated files are newer than configure
configure:10040: result: done
configure:10107: creating ./config.status

----------------------

Running config.status.

----------------------

This file was extended by neko config.status 0.7.2, which was
generated by GNU Autoconf 2.69. Invocation command line was

CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status

on wzc-X11DPG-OT

config.status:927: creating Makefile
config.status:927: creating src/Makefile
config.status:927: creating tests/Makefile
config.status:927: creating src/comm/comm.F90
config.status:927: creating src/config/neko_config.f90
config.status:927: creating src/config/num_types.f90
config.status:927: creating src/device/device_config.h
config.status:927: creating src/scripts/cltostring.sh
config.status:927: creating makeneko
config.status:927: creating neko.pc
config.status:927: creating tests/stack/Makefile
config.status:927: creating tests/tuple/Makefile
config.status:927: creating tests/point/Makefile
config.status:927: creating tests/htable/Makefile
config.status:927: creating tests/uset/Makefile
config.status:927: creating tests/quad/Makefile
config.status:927: creating tests/hex/Makefile
config.status:927: creating tests/tet/Makefile
config.status:927: creating tests/tri/Makefile
config.status:927: creating tests/math/Makefile
config.status:927: creating tests/mesh/Makefile
config.status:927: creating tests/space/Makefile
config.status:927: creating tests/dofmap/Makefile
config.status:927: creating tests/field/Makefile
config.status:927: creating tests/mean_field/Makefile
config.status:927: creating tests/mean_sqr_field/Makefile
config.status:927: creating tests/gather_scatter/Makefile
config.status:927: creating tests/krylov/Makefile
config.status:927: creating tests/bc/Makefile
config.status:927: creating tests/signal/Makefile
config.status:927: creating tests/jobctrl/Makefile
config.status:927: creating tests/device/Makefile
config.status:927: creating tests/device_math/Makefile
config.status:927: creating tests/mathops/Makefile
config.status:927: creating tests/device_mathops/Makefile
config.status:927: creating tests/octree/Makefile
config.status:927: creating tests/vector/Makefile
config.status:927: creating tests/scratch_registry/Makefile
config.status:927: creating tests/fast3d/Makefile
config.status:927: creating tests/time_scheme/Makefile
config.status:927: creating tests/time_scheme_controller/Makefile
config.status:927: creating tests/time_based_controller/Makefile
config.status:927: creating tests/point_interpolation/Makefile
config.status:927: creating contrib/Makefile
config.status:927: creating contrib/rea2nbin/Makefile
config.status:927: creating contrib/genmeshbox/Makefile
config.status:927: creating contrib/average_fields_in_time/Makefile
config.status:927: creating contrib/postprocess_fluid_stats/Makefile
config.status:927: creating contrib/average_field_in_space/Makefile
config.status:927: creating contrib/prepart/Makefile
config.status:927: creating doc/Doxyfile
config.status:927: creating doc/Makefile
config.status:1099: executing depfiles commands

----------------

Cache variables.

----------------

ac_cv_build=x86_64-pc-linux-gnu
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=gcc
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=
ac_cv_env_CXX_value=
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=set
ac_cv_env_FC_value=gfortran
ac_cv_env_JSON_Fortran_CFLAGS_set=
ac_cv_env_JSON_Fortran_CFLAGS_value=
ac_cv_env_JSON_Fortran_LIBS_set=
ac_cv_env_JSON_Fortran_LIBS_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_MPICC_set=set
ac_cv_env_MPICC_value=mpicc
ac_cv_env_MPICXX_set=
ac_cv_env_MPICXX_value=
ac_cv_env_MPIFC_set=set
ac_cv_env_MPIFC_value=mpif90
ac_cv_env_PKG_CONFIG_LIBDIR_set=
ac_cv_env_PKG_CONFIG_LIBDIR_value=
ac_cv_env_PKG_CONFIG_PATH_set=
ac_cv_env_PKG_CONFIG_PATH_value=
ac_cv_env_PKG_CONFIG_set=
ac_cv_env_PKG_CONFIG_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_libxsmmf_CFLAGS_set=
ac_cv_env_libxsmmf_CFLAGS_value=
ac_cv_env_libxsmmf_LIBS_set=
ac_cv_env_libxsmmf_LIBS_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_fc_compiler_gnu=yes
ac_cv_fc_pp_srcext_F90=none
ac_cv_func_cheev=yes
ac_cv_header_cpuid_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_parmetis_h=no
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-pc-linux-gnu
ac_cv_lib_cudart_cudaFree=yes
ac_cv_lib_gs_fgslib_gs_setup=yes
ac_cv_lib_openblas_sgemm=yes
ac_cv_lib_parmetis_ParMETIS_V3_PartMeshKway=no
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_path_NVCC=/usr/local/cuda/bin/nvcc
ac_cv_path_ac_pt_PKG_CONFIG=/usr/bin/pkg-config
ac_cv_path_install='/usr/bin/install -c'
ac_cv_path_mkdir=/usr/bin/mkdir
ac_cv_prog_AWK=mawk
ac_cv_prog_CPP='mpicc -E'
ac_cv_prog_MPICC=mpicc
ac_cv_prog_MPICXX=mpic++
ac_cv_prog_MPIFC=mpif90
ac_cv_prog_ac_ct_CC=gcc
ac_cv_prog_ac_ct_CXX=g++
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_fc_g=yes
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_make_support_nested_variables=yes
am_cv_prog_cc_c_o=yes
ax_cv_fc_compiler_vendor=gnu
pkg_cv_JSON_Fortran_CFLAGS=-I/usr/local/include
pkg_cv_JSON_Fortran_LIBS='-L/usr/local/lib -ljsonfortran'

-----------------

Output variables.

-----------------

ACLOCAL='${SHELL} /home/wzc/neko-0.7.2/missing aclocal-1.15'
ADIOS2CONF=''
AMDEPBACKSLASH=''
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH=''
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AUTOCONF='${SHELL} /home/wzc/neko-0.7.2/missing autoconf'
AUTOHEADER='${SHELL} /home/wzc/neko-0.7.2/missing autoheader'
AUTOMAKE='${SHELL} /home/wzc/neko-0.7.2/missing automake-1.15'
AWK='mawk'
BLAS_LIBS='-lopenblas'
CC='mpicc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CPP='mpicc -E'
CPPFLAGS=' '
CUDA_ARCH='-arch=sm_80'
CUDA_CFLAGS='-O3'
CXX='mpic++'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS='-g -O2'
CYGPATH_W='echo'
DARSHAN_LIBS=''
DEFS='-DPACKAGE_NAME="neko" -DPACKAGE_TARNAME="neko" -DPACKAGE_VERSION="0.7.2" -DPACKAGE_STRING="neko\ 0.7.2" -DPACKAGE_BUGREPORT="" -DPACKAGE_URL="" -DPACKAGE="neko" -DVERSION="0.7.2" -DHAVE_DERIVED_TYPE_IO=1 -DHAVE_REAL128=1 -DHAVE_MPI_F08=1 -DHAVE_MPI_PARAM_DTYPE=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_CPUID_H=1 -DHAVE_BLAS=1 -DHAVE_LAPACK=1 -DHAVE_GSLIB=1 -DHAVE_CUDA=1'
DEPDIR='.deps'
DOXYGEN=''
DOXYGEN_DEPS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP='/usr/bin/grep -E'
ENABLE_ADIOS2_FALSE=''
ENABLE_ADIOS2_TRUE='#'
ENABLE_CUDA_FALSE='#'
ENABLE_CUDA_TRUE=''
ENABLE_DOXYGEN_FALSE=''
ENABLE_DOXYGEN_TRUE='#'
ENABLE_FLINT_FALSE=''
ENABLE_FLINT_TRUE='#'
ENABLE_HIP_FALSE=''
ENABLE_HIP_TRUE='#'
ENABLE_MAKEDEPF90_FALSE=''
ENABLE_MAKEDEPF90_TRUE='#'
ENABLE_OPENCL_FALSE=''
ENABLE_OPENCL_TRUE='#'
ENABLE_PARMETIS_FALSE=''
ENABLE_PARMETIS_TRUE='#'
ENABLE_PFUNIT_FALSE=''
ENABLE_PFUNIT_TRUE='#'
EXEEXT=''
FC='mpif90'
FCFLAGS='-I/usr/local/include -g -O2'
FCFLAGS_F90=''
FLINT=''
GREP='/usr/bin/grep'
HIPCC=''
HIP_HIPCC_FLAGS=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
JSON_Fortran_CFLAGS='-I/usr/local/include'
JSON_Fortran_LIBS='-L/usr/local/lib -ljsonfortran'
LAPACK_LIBS=''
LDFLAGS='-L/usr/local/cuda/lib64 -L/home/wzc/gslib-master/build/lib -L/home/wzc/gslib-master/build '
LIBOBJS=''
LIBS='-L/usr/local/lib -ljsonfortran -lcudart -lgs -lopenblas '
LTLIBOBJS=''
MAINT='#'
MAINTAINER_MODE_FALSE=''
MAINTAINER_MODE_TRUE='#'
MAKEDEPF90=''
MAKEINFO='${SHELL} /home/wzc/neko-0.7.2/missing makeinfo'
METIS_LIBS=''
MKDIR_P='/usr/bin/mkdir -p'
MPICC='mpicc'
MPICXX='mpic++'
MPIFC='mpif90'
MPILIBS=' '
NEKO_BUILD_INFO='(build: 2024-05-07 on x86_64-pc-linux-gnu using gnu)'
NEKO_C_REAL_TYPE='c_double'
NEKO_DEV_REAL_TYPE='double'
NEKO_MPI_REAL_TYPE='MPI_DOUBLE_PRECISION'
NEKO_REAL128_TYPE='REAL128'
NEKO_REAL_TYPE='dp'
NVCC='/usr/local/cuda/bin/nvcc'
OBJEXT='o'
PACKAGE='neko'
PACKAGE_BUGREPORT=''
PACKAGE_NAME='neko'
PACKAGE_STRING='neko 0.7.2'
PACKAGE_TARNAME='neko'
PACKAGE_URL=''
PACKAGE_VERSION='0.7.2'
PARMETIS_LIBS=''
PATH_SEPARATOR=':'
PFUNIT_DIR=''
PKG_CONFIG='/usr/bin/pkg-config'
PKG_CONFIG_LIBDIR=''
PKG_CONFIG_PATH=''
RANLIB='ranlib'
SET_MAKE=''
SHELL='/bin/bash'
STRIP=''
VERSION='0.7.2'
ac_ct_CC='gcc'
ac_ct_CXX='g++'
ac_ct_FC=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep='_no'
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
blk_size='10000'
build='x86_64-pc-linux-gnu'
build_alias=''
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='pc'
cuda_bcknd='1'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
device_bcknd='1'
device_mpi='.false.'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
have_adios2=''
have_cray_accel=''
have_cray_libsci=''
have_cray_parmetis=''
have_cuda='yes'
have_gslib='yes'
have_hip=''
have_nccl=''
have_nvtx=''
have_opencl=''
have_rccl=''
have_roctx=''
hip_bcknd='0'
host='x86_64-pc-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /home/wzc/neko-0.7.2/install-sh'
is_cray='no'
is_hpe_cray='no'
is_sx='0'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
libxsmmf_CFLAGS=''
libxsmmf_LIBS=''
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='$(MKDIR_P)'
nccl_bcknd='0'
nvtx_bcknd='0'
oldincludedir='/usr/include'
opencl_bcknd='0'
pdfdir='${docdir}'
prefix='/home/wzc/neko-0.7.2/installation'
program_transform_name='s,x,x,'
psdir='${docdir}'
rccl_bcknd='0'
roctx_bcknd='0'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
xsmm_bcknd='0'

-----------

confdefs.h.

-----------

/* confdefs.h */
#define PACKAGE_NAME "neko"
#define PACKAGE_TARNAME "neko"
#define PACKAGE_VERSION "0.7.2"
#define PACKAGE_STRING "neko 0.7.2"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""
#define PACKAGE "neko"
#define VERSION "0.7.2"
#define HAVE_DERIVED_TYPE_IO 1
#define HAVE_REAL128 1
#define HAVE_MPI_F08 1
#define HAVE_MPI_PARAM_DTYPE 1
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_CPUID_H 1
#define HAVE_BLAS 1
#define HAVE_LAPACK 1
#define HAVE_GSLIB 1
#define HAVE_CUDA 1

configure: exit 0

2 replies

adperezm May 7, 2024
Collaborator

I see, I have a perhaps stupid question. If you do not set the visible devices environmental variable and then run with only one mpirank. Does it still segfaults?

vanchisen May 7, 2024
Author

Yes same segfaults error

vanchisen · 2024-05-07T21:49:29Z

vanchisen
May 7, 2024
Author

Hi All,

I just figured out that if I compile neko in the docker container that was used for running nekRS can partially slove the segfault problem,
But as I try to run the turbpipe case in multiple GPUs, it doesn't work properly. I check with nividia-smi, only one GPU is utlized,
In order to run neko, I have used following two commands,

./makeneko pipe.f90

mpirun -np 4 ./neko pipe.case >& out &

Any hints about multiple GPUs ?

2 replies

njansson May 8, 2024
Maintainer

For multiple GPUs you need to manually assign each gpu to an mpi rank. Typically done via a wrapper script defining CUDA_VISIBLE_DEVICES for each rank. See for example,

https://github.com/ExtremeFLOW/flettner_rotor/blob/main/run.sh

vanchisen May 8, 2024
Author

Thank you Niclas, it works !

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Segmentation fault invalid memory reference #1270

{{title}}

Replies: 6 comments 6 replies

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

Select a reply

Segmentation fault invalid memory reference #1270

vanchisen May 7, 2024

Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted.

mpirun noticed that process rank 0 with PID 0 on node wzc-X11DPG-OT exited on signal 11 (Segmentation fault).

Replies: 6 comments · 6 replies

njansson May 7, 2024 Maintainer

vanchisen May 7, 2024 Author

adperezm May 7, 2024 Collaborator

vanchisen May 7, 2024 Author

adperezm May 7, 2024 Collaborator

njansson May 7, 2024 Maintainer

vanchisen May 7, 2024 Author

---------

Platform.

---------

-----------

Core tests.

-----------

----------------------

Running config.status.

----------------------

----------------

Cache variables.

----------------

-----------------

Output variables.

-----------------

-----------

confdefs.h.

-----------

adperezm May 7, 2024 Collaborator

vanchisen May 7, 2024 Author

vanchisen May 7, 2024 Author

njansson May 8, 2024 Maintainer

vanchisen May 8, 2024 Author

vanchisen
May 7, 2024

Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.

Replies: 6 comments 6 replies

njansson
May 7, 2024
Maintainer

vanchisen
May 7, 2024
Author

adperezm May 7, 2024
Collaborator

vanchisen
May 7, 2024
Author

adperezm May 7, 2024
Collaborator

njansson
May 7, 2024
Maintainer

vanchisen
May 7, 2024
Author

adperezm May 7, 2024
Collaborator

vanchisen May 7, 2024
Author

vanchisen
May 7, 2024
Author

njansson May 8, 2024
Maintainer

vanchisen May 8, 2024
Author