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../externals/cgns/hdf5/H5public.h:63:10: fatal error: mpi.h: No such file or director |
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November 22, 2023, 23:30
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../externals/cgns/hdf5/H5public.h:63:10: fatal error: mpi.h: No such file or director
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#1 |
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New Member
Mohsin
Join Date: Jul 2023
Posts: 21
Rep Power: 3  |
Hi i am trying to compile su2 for parallel support. but I am getting this error
Code:
[9/1078] Compiling C object externals/cgns/hdf5/libsu2hdf5.a.p/H5A.c.o
FAILED: externals/cgns/hdf5/libsu2hdf5.a.p/H5A.c.o
cc -Iexternals/cgns/hdf5/libsu2hdf5.a.p -Iexternals/cgns/hdf5 -I../externals/cgns/hdf5 -fdiagnostics-color=always -std=c99 -g -fPIC -Wno-unused-result -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable -Wno-sign-compare -Wno-stringop-overflow -Wno-error=discarded-qualifiers -Wno-error=maybe-uninitialized -Wno-error=unused-function -Wno-error=unused-label -Wno-pedantic -Wno-error=stringop-truncation -Wno-error=cast-function-type -Wno-stringop-truncation -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -D_GNU_SOURCE -MD -MQ externals/cgns/hdf5/libsu2hdf5.a.p/H5A.c.o -MF externals/cgns/hdf5/libsu2hdf5.a.p/H5A.c.o.d -o externals/cgns/hdf5/libsu2hdf5.a.p/H5A.c.o -c ../externals/cgns/hdf5/H5A.c
In file included from ../externals/cgns/hdf5/H5private.h:27,
from ../externals/cgns/hdf5/H5A.c:24:
../externals/cgns/hdf5/H5public.h:63:10: fatal error: mpi.h: No such file or directory
63 | #include <mpi.h>
| ^~~~~~~
compilation terminated.
[10/1078] Compiling C object externals/cgns/hdf5/libsu2hdf5.a.p/H5Abtree2.c.o
FAILED: externals/cgns/hdf5/libsu2hdf5.a.p/H5Abtree2.c.o
cc -Iexternals/cgns/hdf5/libsu2hdf5.a.p -Iexternals/cgns/hdf5 -I../externals/cgns/hdf5 -fdiagnostics-color=always -std=c99 -g -fPIC -Wno-unused-result -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable -Wno-sign-compare -Wno-stringop-overflow -Wno-error=discarded-qualifiers -Wno-error=maybe-uninitialized -Wno-error=unused-function -Wno-error=unused-label -Wno-pedantic -Wno-error=stringop-truncation -Wno-error=cast-function-type -Wno-stringop-truncation -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -D_GNU_SOURCE -MD -MQ externals/cgns/hdf5/libsu2hdf5.a.p/H5Abtree2.c.o -MF externals/cgns/hdf5/libsu2hdf5.a.p/H5Abtree2.c.o.d -o externals/cgns/hdf5/libsu2hdf5.a.p/H5Abtree2.c.o -c ../externals/cgns/hdf5/H5Abtree2.c
In file included from ../externals/cgns/hdf5/H5private.h:27,
from ../externals/cgns/hdf5/H5Abtree2.c:34:
../externals/cgns/hdf5/H5public.h:63:10: fatal error: mpi.h: No such file or directory
63 | #include <mpi.h>
| ^~~~~~~
compilation terminated.
[11/1078] Compiling C object externals/cgns/hdf5/libsu2hdf5.a.p/H5trace.c.o
FAILED: externals/cgns/hdf5/libsu2hdf5.a.p/H5trace.c.o
cc -Iexternals/cgns/hdf5/libsu2hdf5.a.p -Iexternals/cgns/hdf5 -I../externals/cgns/hdf5 -fdiagnostics-color=always -std=c99 -g -fPIC -Wno-unused-result -Wno-unused-parameter -Wno-unused-variable -Wno-unused-but-set-variable -Wno-sign-compare -Wno-stringop-overflow -Wno-error=discarded-qualifiers -Wno-error=maybe-uninitialized -Wno-error=unused-function -Wno-error=unused-label -Wno-pedantic -Wno-error=stringop-truncation -Wno-error=cast-function-type -Wno-stringop-truncation -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -D_GNU_SOURCE -MD -MQ externals/cgns/hdf5/libsu2hdf5.a.p/H5trace.c.o -MF externals/cgns/hdf5/libsu2hdf5.a.p/H5trace.c.o.d -o externals/cgns/hdf5/libsu2hdf5.a.p/H5trace.c.o -c ../externals/cgns/hdf5/H5trace.c
In file included from ../externals/cgns/hdf5/H5private.h:27,
from ../externals/cgns/hdf5/H5trace.c:34:
../externals/cgns/hdf5/H5public.h:63:10: fatal error: mpi.h: No such file or directory
63 | #include <mpi.h>
| ^~~~~~~
compilation terminated.
ninja: build stopped: subcommand failed.
First of all I compiled it for serial support and i did not get any error, using the following commands: Code:
./meson.py build ./ninja -C build install Code:
./meson.py build --reconfigure -Dcustom-mpi=true -Dextra-deps=mpich -Denable-autodiff=true --buildtype=debug Code:
git command not found. Using fall-back method to init submodules
The Meson build system
Version: 0.61.1
Source dir: /home/mohsin/Downloads/SU2-7.5.1
Build dir: /home/mohsin/Downloads/SU2-7.5.1/build
Build type: native build
Project name: SU2
Project version: 7.5.1 "Blackbird"
C compiler for the host machine: cc (gcc 11.4.0 "cc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
C linker for the host machine: cc ld.bfd 2.38
C++ compiler for the host machine: c++ (gcc 11.4.0 "c++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
C++ linker for the host machine: c++ ld.bfd 2.38
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python3 found: YES (/home/mohsin/anaconda3/bin/python3)
WARNING: Python files installed by Meson might not be found by python interpreter.
This warning can be avoided by setting "python.platlibdir" option.
WARNING: Python files installed by Meson might not be found by python interpreter.
This warning can be avoided by setting "python.purelibdir" option.
Compiler for C++ supports arguments -Wno-ignored-qualifiers: YES (cached)
Compiler for C++ supports arguments -Wno-unused-parameter: YES (cached)
Compiler for C++ supports arguments -Wno-deprecated-declarations: YES (cached)
Compiler for C++ supports arguments -Wno-error=cast-function-type: YES (cached)
Compiler for C++ supports arguments -Wno-cast-function-type: YES (cached)
Compiler for C++ supports arguments -Wno-error=stringop-truncation: YES (cached)
Compiler for C++ supports arguments -Wno-stringop-truncation: YES (cached)
Compiler for C++ supports arguments -Wno-error=missing-field-initializers: YES (cached)
Compiler for C++ supports arguments -Wno-missing-field-initializers: YES (cached)
Compiler for C++ supports arguments -Wno-error=class-memaccess: YES (cached)
Compiler for C++ supports arguments -Wno-class-memaccess: YES (cached)
Compiler for C++ supports arguments -Wno-unused-result: YES (cached)
Compiler for C++ supports arguments -Wno-unused-parameter: YES (cached)
Compiler for C++ supports arguments -Wno-unused-variable: YES (cached)
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES (cached)
Compiler for C++ supports arguments -Wno-sign-compare: YES (cached)
Compiler for C++ supports arguments -Wno-error=unused-function: YES (cached)
Compiler for C++ supports arguments -Wno-pedantic: YES (cached)
Compiler for C++ supports arguments -Wno-error=stringop-truncation: YES (cached)
Compiler for C++ supports arguments -Wno-stringop-truncation: YES (cached)
Compiler for C++ supports arguments -Wno-error=absolute-value: YES (cached)
Compiler for C++ supports arguments -Wno-error=class-memaccess: YES (cached)
Compiler for C++ supports arguments -Wno-unused-result: YES (cached)
Compiler for C++ supports arguments -Wno-unused-parameter: YES (cached)
Compiler for C++ supports arguments -Wno-unused-variable: YES (cached)
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES (cached)
Compiler for C++ supports arguments -Wno-sign-compare: YES (cached)
Compiler for C++ supports arguments -Wno-stringop-overflow: YES (cached)
Compiler for C++ supports arguments -Wno-error=discarded-qualifiers: YES (cached)
Compiler for C++ supports arguments -Wno-error=maybe-uninitialized: YES (cached)
Compiler for C++ supports arguments -Wno-error=unused-function: YES (cached)
Compiler for C++ supports arguments -Wno-error=unused-label: YES (cached)
Compiler for C++ supports arguments -Wno-pedantic: YES (cached)
Compiler for C++ supports arguments -Wno-error=stringop-truncation: YES (cached)
Compiler for C++ supports arguments -Wno-error=cast-function-type: YES (cached)
Compiler for C++ supports arguments -Wno-stringop-truncation: YES (cached)
Dependency zlib found: YES 1.2.11 (cached)
Found pkg-config: /usr/bin/pkg-config (0.29.2)
Did not find CMake 'cmake'
Found CMake: NO
Run-time dependency szip found: NO (tried pkgconfig and cmake)
Has header "zlib.h" : YES (cached)
Checking for function "inflate" with dependency zlib: YES (cached)
Has header "sys/file.h" : YES (cached)
Has header "sys/ioctl.h" : YES (cached)
Has header "sys/resource.h" : YES (cached)
Has header "sys/socket.h" : YES (cached)
Has header "sys/stat.h" : YES (cached)
Has header "sys/time.h" : YES (cached)
Has header "sys/types.h" : YES (cached)
Has header "features.h" : YES (cached)
Has header "dirent.h" : YES (cached)
Has header "setjmp.h" : YES (cached)
Has header "stddef.h" : YES (cached)
Has header "stdint.h" : YES (cached)
Has header "unistd.h" : YES (cached)
Has header "io.h" : NO (cached)
Has header "winsock2.h" : NO (cached)
Has header "globus/common.h" : NO (cached)
Has header "pdb.h" : NO (cached)
Has header "pthread.h" : YES (cached)
Has header "srbclient.h" : NO (cached)
Has header "string.h" : YES (cached)
Has header "strings.h" : YES (cached)
Has header "stdlib.h" : YES (cached)
Has header "memory.h" : YES (cached)
Has header "dlfcn.h" : YES (cached)
Has header "inttypes.h" : YES (cached)
Has header "netinet/in.h" : YES (cached)
Has header "netdb.h" : YES (cached)
Has header "arpa/inet.h" : YES (cached)
Has header "stdbool.h" : YES (cached)
Has header "quadmath.h" : YES (cached)
Library m found: YES
Checking for function "ceil" with dependency -lm: YES (cached)
Library dl found: YES
Checking for function "dlopen" with dependency -ldl: YES (cached)
Library ucb found: NO
Checking for function "gethostbyname" with dependency -lucb: NO (cached)
Checking for function "lseek64" : NO (cached)
Checking for function "fseeko" : NO (cached)
Checking for function "stat64" : NO (cached)
Checking for size of "char" : 1
Checking for size of "short" : 2
Checking for size of "int" : 4
Checking for size of "unsigned" : 4
Checking for size of "long" : 8
Checking for size of "long long" : 8
Checking for size of "__int64" : -1
Checking for size of "float" : 4
Checking for size of "double" : 8
Checking for size of "long double" : 16
Checking for size of "int8_t" : 1
Checking for size of "uint8_t" : 1
Checking for size of "int_least8_t" : 1
Checking for size of "uint_least8_t" : 1
Checking for size of "int_fast8_t" : 1
Checking for size of "uint_fast8_t" : 1
Checking for size of "int16_t" : 2
Checking for size of "uint16_t" : 2
Checking for size of "int_least16_t" : 2
Checking for size of "uint_least16_t" : 2
Checking for size of "int_fast16_t" : 8
Checking for size of "uint_fast16_t" : 8
Checking for size of "int32_t" : 4
Checking for size of "uint32_t" : 4
Checking for size of "int_least32_t" : 4
Checking for size of "uint_least32_t" : 4
Checking for size of "int_fast32_t" : 8
Checking for size of "uint_fast32_t" : 8
Checking for size of "int64_t" : 8
Checking for size of "uint64_t" : 8
Checking for size of "int_least64_t" : 8
Checking for size of "uint_least64_t" : 8
Checking for size of "int_fast64_t" : 8
Checking for size of "uint_fast64_t" : 8
Checking for size of "size_t" : 8
Checking for size of "ssize_t" : -1
Checking for size of "ptrdiff_t" : -1
Checking for size of "off_t" : 8
Checking for size of "off64_t" : -1
Checking for size of "time_t" : 8
Checking for size of "bool" : 1
Checking for size of "_Quad" : -1
Checking for size of "__float128" : 16
Checking if "check dev_t" : compiles: YES (cached)
Checking if "check dev_t scalar" runs: YES
Checking if "CLOCK_MONOTONIC" : compiles: YES (cached)
Checking whether type "struct tm" has member "tm_gmtoff" : NO (cached)
Checking whether type "struct tm" has member "__tm_gmtoff" : YES (cached)
Checking whether type "struct tm" has member "tm_sec" : YES (cached)
Checking whether type "struct tm" has member "tz_minuteswest" : NO (cached)
Checking for function "gettimeofday" : YES (cached)
Checking whether type "struct stat" has member "st_blocks" : YES (cached)
Checking for function "ioctl" : YES (cached)
Header <sys/ioctl.h> has symbol "TIOCGWINSZ" : YES (cached)
Header <sys/ioctl.h> has symbol "TIOCGETD" : YES (cached)
Checking for function "getpwuid" : YES (cached)
Checking for function "alarm" : YES (cached)
Checking for function "fcntl" : YES (cached)
Checking for function "flock" : YES (cached)
Checking for function "fork" : YES (cached)
Checking for function "frexpf" : YES (cached)
Checking for function "frexpl" : YES (cached)
Checking for function "gethostname" : YES (cached)
Checking for function "getrusage" : YES (cached)
Checking for function "llround" : YES (cached)
Checking for function "llroundf" : YES (cached)
Checking for function "lround" : YES (cached)
Checking for function "lroundf" : YES (cached)
Checking for function "lstat" : YES (cached)
Checking for function "pread" : YES (cached)
Checking for function "pwrite" : YES (cached)
Checking for function "rand_r" : YES (cached)
Checking for function "random" : YES (cached)
Checking for function "round" : YES (cached)
Checking for function "roundf" : YES (cached)
Checking for function "setsysinfo" : NO (cached)
Checking for function "signal" : YES (cached)
Checking for function "longjmp" : YES (cached)
Checking for function "setjmp" : YES (cached)
Checking for function "siglongjmp" : YES (cached)
Checking for function "sigsetjmp" : NO (cached)
Checking for function "sigprocmask" : YES (cached)
Checking for function "snprintf" : YES (cached)
Checking for function "srandom" : YES (cached)
Checking for function "strdup" : YES (cached)
Checking for function "strtoll" : YES (cached)
Checking for function "strtoull" : YES (cached)
Checking for function "symlink" : YES (cached)
Checking for function "system" : YES (cached)
Checking for function "tmpfile" : YES (cached)
Checking for function "asprintf" : YES (cached)
Checking for function "vasprintf" : YES (cached)
Checking for function "waitpid" : YES (cached)
Checking for function "vsnprintf" : YES (cached)
Header <setjmp.h> has symbol "sigsetjmp" : NO (cached)
Checking if "inline keyword check" : compiles: YES (cached)
Configuring H5pubconf.h using configuration
Checking for size of "long" : 8
Checking for size of "void *" : 8
Configuring cgnstypes.h using configuration
Configuring cg_hash_types.h using configuration
Configuring cgnsconfig.h using configuration
Compiler for C++ supports arguments -Wno-unused-result: YES (cached)
Compiler for C++ supports arguments -Wno-unused-parameter: YES (cached)
Compiler for C++ supports arguments -Wno-unused-variable: YES (cached)
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES (cached)
Compiler for C++ supports arguments -Wno-unknown-pragmas: YES (cached)
Compiler for C++ supports arguments -Wno-sign-compare: YES (cached)
Compiler for C++ supports arguments -Wno-clobbered: YES (cached)
Compiler for C++ supports arguments -Wno-empty-body: YES (cached)
Compiler for C++ supports arguments -Wno-unused-label: YES (cached)
Compiler for C++ supports arguments -Wno-misleading-indentation: YES (cached)
Compiler for C++ supports arguments -Wno-maybe-uninitialized: YES (cached)
Compiler for C++ supports arguments -Wno-pedantic: YES (cached)
Compiler for C++ supports arguments -Wno-error=absolute-value: YES (cached)
Compiler for C++ supports arguments -Wno-absolute-value: NO (cached)
WARNING: You should add the boolean check kwarg to the run_command call.
It currently defaults to false,
but it will default to true in future releases of meson.
See also: https://github.com/mesonbuild/meson/issues/9300
Message: Boost sources found.
Compiler for C++ supports arguments -Wno-misleading-indentation: YES (cached)
Compiler for C++ supports arguments -Wno-uninitialized: YES (cached)
Compiler for C++ supports arguments -Wno-placement-new: YES (cached)
Compiler for C++ supports arguments -Wno-pedantic: YES (cached)
Compiler for C++ supports arguments -Wno-error=class-memaccess: YES (cached)
Compiler for C++ supports arguments -Wno-class-memaccess: YES (cached)
Compiler for C++ supports arguments -Wno-error=deprecated-copy: YES (cached)
Compiler for C++ supports arguments -Wno-deprecated-copy: YES (cached)
Compiler for C++ supports arguments -Wno-error=cast-function-type: YES (cached)
Compiler for C++ supports arguments -Wno-cast-function-type: YES (cached)
Run-time dependency mpich found: YES 4.0
Message: -------------------------------------------------------------------------
| ___ _ _ ___ |
| / __| | | |_ ) Release 7.5.1 "Blackbird" |
| \__ \ |_| |/ / |
| |___/\___//___| Meson Configuration Summary |
| |
-------------------------------------------------------------------------
Option Value
---------------------
TecIO: true
CGNS: true
AD (reverse): true
AD (forward): false
Python Wrapper: false
Intel-MKL: false
OpenBlas: false
PaStiX: false
Mixed Float: false
libROM: false
CoolProp: false
Please be sure to add the $SU2_HOME and $SU2_RUN environment variables,
and update your $PATH (and $PYTHONPATH if applicable) with $SU2_RUN
Based on the input to this configuration, add these lines to your .bashrc file:
export SU2_RUN=/usr/local/bin
export SU2_HOME=/home/mohsin/Downloads/SU2-7.5.1
export PATH=$PATH:$SU2_RUN
export PYTHONPATH=$PYTHONPATH:$SU2_RUN
Use './ninja -C build install' to compile and install SU2
Build targets in project: 20
SU2 7.5.1 "Blackbird"
User defined options
buildtype : debug
custom-mpi : true
enable-autodiff: true
extra-deps : mpich
Found ninja-1.10.0.git at /home/mohsin/Downloads/SU2-7.5.1/ninja
ubuntu 22.04 anaconda3 python 3.11.4 SU2-7.5.1 Can somebody help me to solve this issue please. |
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November 23, 2023, 02:54
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#2 |
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Senior Member
bigfoot
Join Date: Dec 2011
Location: Netherlands
Posts: 657
Rep Power: 19 |
It's complaining about mpi, so you probably do not have it installed. Was compilation without mpi successful?
If that is the problem, install either mpich or openmpi, and install the develop package, which contains the header files. |
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November 23, 2023, 16:40
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#3 |
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New Member
Join Date: Mar 2022
Posts: 5
Rep Power: 4 |
Hello, I am having the same issues with SU2 v8.0.0 (branch new_turbo_outputs). I could compile for single core simulations, but could not compile for parallel process. Although I have installed mpich and openmpi, I'm still not being able to compile it for mpi.
murillo@DELL_XPS:/mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2$ whereis mpich mpich: /usr/lib/x86_64-linux-gnu/mpich murillo@DELL_XPS:/mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2$ whereis openmpi openmpi: /usr/lib/x86_64-linux-gnu/openmpi /etc/openmpi /usr/share/openmpi My computer is running with Windows 11, but I'm doing all configuration using Windows Subsystem for Linux (WSL) and using Ubuntu as operational system. Previously this computed had ANSYS CFX with MPI installed, but I have uninstalled it. Please let me know if you have any additional tips or suggestions that might help. |
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November 23, 2023, 18:41
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#4 |
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Senior Member
bigfoot
Join Date: Dec 2011
Location: Netherlands
Posts: 657
Rep Power: 19 |
During the meson run you can check if the compiler uses mpi. It should look something like below, if it is just saying it uses mpicc then it did not detect the mpi installation.
Code:
C compiler for the host machine: /usr/bin/mpicc.mpich (gcc 11.4.0 "gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0") C linker for the host machine: /usr/bin/mpicc.mpich ld.bfd 2.38 If you have multiple mpi versions, you can make sure that the correct one is linked using: Code:
$ update-alternatives --config mpirun There are 3 choices for the alternative mpirun (providing /usr/bin/mpirun). Selection Path Priority Status ------------------------------------------------------------ 0 /usr/bin/mpirun.openmpi 50 auto mode 1 /usr/bin/mpirun.lam 30 manual mode * 2 /usr/bin/mpirun.mpich 40 manual mode 3 /usr/bin/mpirun.openmpi 50 manual mode Press <enter> to keep the current choice[*], or type selection number: |
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November 24, 2023, 12:01
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#5 |
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New Member
Join Date: Mar 2022
Posts: 5
Rep Power: 4 |
I updated the mpirun configurations as suggested:
Code:
murillo@DELL_XPS:/usr/bin$ sudo update-alternatives --config mpirun [sudo] password for murillo: There are 2 choices for the alternative mpirun (providing /usr/bin/mpirun). Selection Path Priority Status ------------------------------------------------------------ * 0 /usr/bin/mpirun.openmpi 50 auto mode 1 /usr/bin/mpirun.mpich 40 manual mode 2 /usr/bin/mpirun.openmpi 50 manual mode Press <enter> to keep the current choice[*], or type selection number: 1 update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in manual mode murillo@DELL_XPS:/usr/bin$ sudo update-alternatives --config mpirun There are 2 choices for the alternative mpirun (providing /usr/bin/mpirun). Selection Path Priority Status ------------------------------------------------------------ 0 /usr/bin/mpirun.openmpi 50 auto mode * 1 /usr/bin/mpirun.mpich 40 manual mode 2 /usr/bin/mpirun.openmpi 50 manual mode Press <enter> to keep the current choice[*], or type selection number: Code:
python3 meson.py build --reconfigure -Dcustom-mpi=true -Dwith-mpi=enabled -Denable-autodiff=true Code:
Project version: 8.0.0 "Harrier" C compiler for the host machine: cc (gcc 11.4.0 "cc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0") C linker for the host machine: cc ld.bfd 2.38 C++ compiler for the host machine: c++ (gcc 11.4.0 "c++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0") C++ linker for the host machine: c++ ld.bfd 2.38 Code:
python3 meson.py build --reconfigure -Dcustom-mpi=true -Dextra-deps=mpich -Dwith-mpi=enabled -Denable-autodiff=true This is the complete meson output: Code:
murillo@DELL_XPS:/mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2$ python3 meson.py build --reconfigure -Dcustom-mpi=true -Dwith-mpi=enabled -Denable-autodiff=true
update CoolProp
/mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2/subprojects/CoolProp
/mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2
CoolProp updated
The Meson build system
Version: 0.61.1
Source dir: /mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2
Build dir: /mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2/build
Build type: native build
Project name: SU2
Project version: 8.0.0 "Harrier"
C compiler for the host machine: cc (gcc 11.4.0 "cc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
C linker for the host machine: cc ld.bfd 2.38
C++ compiler for the host machine: c++ (gcc 11.4.0 "c++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0")
C++ linker for the host machine: c++ ld.bfd 2.38
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python3 found: YES (/usr/bin/python3)
WARNING: Python files installed by Meson might not be found by python interpreter.
This warning can be avoided by setting "python.platlibdir" option.
WARNING: Python files installed by Meson might not be found by python interpreter.
This warning can be avoided by setting "python.purelibdir" option.
Compiler for C++ supports arguments -Wno-ignored-qualifiers: YES (cached)
Compiler for C++ supports arguments -Wno-unused-parameter: YES (cached)
Compiler for C++ supports arguments -Wno-deprecated-declarations: YES (cached)
Compiler for C++ supports arguments -Wno-error=cast-function-type: YES (cached)
Compiler for C++ supports arguments -Wno-cast-function-type: YES (cached)
Compiler for C++ supports arguments -Wno-error=stringop-truncation: YES (cached)
Compiler for C++ supports arguments -Wno-stringop-truncation: YES (cached)
Compiler for C++ supports arguments -Wno-error=missing-field-initializers: YES (cached)
Compiler for C++ supports arguments -Wno-missing-field-initializers: YES (cached)
Compiler for C++ supports arguments -Wno-error=class-memaccess: YES (cached)
Compiler for C++ supports arguments -Wno-class-memaccess: YES (cached)
Compiler for C supports arguments -Wno-unused-result: YES (cached)
Compiler for C supports arguments -Wno-unused-parameter: YES (cached)
Compiler for C supports arguments -Wno-unused-variable: YES (cached)
Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached)
Compiler for C supports arguments -Wno-sign-compare: YES (cached)
Compiler for C supports arguments -Wno-error=unused-function: YES (cached)
Compiler for C supports arguments -Wno-pedantic: YES (cached)
Compiler for C supports arguments -Wno-error=stringop-truncation: YES (cached)
Compiler for C supports arguments -Wno-stringop-truncation: YES (cached)
Compiler for C supports arguments -Wno-error=absolute-value: YES (cached)
Compiler for C supports arguments -Wno-error=class-memaccess: YES (cached)
Compiler for C supports arguments -Wno-unused-result: YES (cached)
Compiler for C supports arguments -Wno-unused-parameter: YES (cached)
Compiler for C supports arguments -Wno-unused-variable: YES (cached)
Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached)
Compiler for C supports arguments -Wno-sign-compare: YES (cached)
Compiler for C supports arguments -Wno-stringop-overflow: YES (cached)
Compiler for C supports arguments -Wno-error=discarded-qualifiers: YES (cached)
Compiler for C supports arguments -Wno-error=maybe-uninitialized: YES (cached)
Compiler for C supports arguments -Wno-error=unused-function: YES (cached)
Compiler for C supports arguments -Wno-error=unused-label: YES (cached)
Compiler for C supports arguments -Wno-pedantic: YES (cached)
Compiler for C supports arguments -Wno-error=stringop-truncation: YES (cached)
Compiler for C supports arguments -Wno-error=cast-function-type: YES (cached)
Compiler for C supports arguments -Wno-stringop-truncation: YES (cached)
Dependency zlib found: YES 1.2.11 (cached)
Found pkg-config: /usr/bin/pkg-config (0.29.2)
Found CMake: /home/murillo/.local/bin/cmake (3.27.7)
Run-time dependency szip found: NO (tried pkgconfig and cmake)
Has header "zlib.h" : YES (cached)
Checking for function "inflate" with dependency zlib: YES (cached)
Has header "sys/file.h" : YES (cached)
Has header "sys/ioctl.h" : YES (cached)
Has header "sys/resource.h" : YES (cached)
Has header "sys/socket.h" : YES (cached)
Has header "sys/stat.h" : YES (cached)
Has header "sys/time.h" : YES (cached)
Has header "sys/types.h" : YES (cached)
Has header "features.h" : YES (cached)
Has header "dirent.h" : YES (cached)
Has header "setjmp.h" : YES (cached)
Has header "stddef.h" : YES (cached)
Has header "stdint.h" : YES (cached)
Has header "unistd.h" : YES (cached)
Has header "io.h" : NO (cached)
Has header "winsock2.h" : NO (cached)
Has header "globus/common.h" : NO (cached)
Has header "pdb.h" : NO (cached)
Has header "pthread.h" : YES (cached)
Has header "srbclient.h" : NO (cached)
Has header "string.h" : YES (cached)
Has header "strings.h" : YES (cached)
Has header "stdlib.h" : YES (cached)
Has header "memory.h" : YES (cached)
Has header "dlfcn.h" : YES (cached)
Has header "inttypes.h" : YES (cached)
Has header "netinet/in.h" : YES (cached)
Has header "netdb.h" : YES (cached)
Has header "arpa/inet.h" : YES (cached)
Has header "stdbool.h" : YES (cached)
Has header "quadmath.h" : YES (cached)
Library m found: YES
Checking for function "ceil" with dependency -lm: YES (cached)
Library dl found: YES
Checking for function "dlopen" with dependency -ldl: YES (cached)
Library ucb found: NO
Checking for function "gethostbyname" with dependency -lucb: NO (cached)
Checking for function "lseek64" : NO (cached)
Checking for function "fseeko" : NO (cached)
Checking for function "stat64" : NO (cached)
Checking for size of "char" : 1
Checking for size of "short" : 2
Checking for size of "int" : 4
Checking for size of "unsigned" : 4
Checking for size of "long" : 8
Checking for size of "long long" : 8
Checking for size of "__int64" : -1
Checking for size of "float" : 4
Checking for size of "double" : 8
Checking for size of "long double" : 16
Checking for size of "int8_t" : 1
Checking for size of "uint8_t" : 1
Checking for size of "int_least8_t" : 1
Checking for size of "uint_least8_t" : 1
Checking for size of "int_fast8_t" : 1
Checking for size of "uint_fast8_t" : 1
Checking for size of "int16_t" : 2
Checking for size of "uint16_t" : 2
Checking for size of "int_least16_t" : 2
Checking for size of "uint_least16_t" : 2
Checking for size of "int_fast16_t" : 8
Checking for size of "uint_fast16_t" : 8
Checking for size of "int32_t" : 4
Checking for size of "uint32_t" : 4
Checking for size of "int_least32_t" : 4
Checking for size of "uint_least32_t" : 4
Checking for size of "int_fast32_t" : 8
Checking for size of "uint_fast32_t" : 8
Checking for size of "int64_t" : 8
Checking for size of "uint64_t" : 8
Checking for size of "int_least64_t" : 8
Checking for size of "uint_least64_t" : 8
Checking for size of "int_fast64_t" : 8
Checking for size of "uint_fast64_t" : 8
Checking for size of "size_t" : 8
Checking for size of "ssize_t" : -1
Checking for size of "ptrdiff_t" : -1
Checking for size of "off_t" : 8
Checking for size of "off64_t" : -1
Checking for size of "time_t" : 8
Checking for size of "bool" : 1
Checking for size of "_Quad" : -1
Checking for size of "__float128" : 16
Checking if "check dev_t" : compiles: YES (cached)
Checking if "check dev_t scalar" runs: NO (1)
Checking if "CLOCK_MONOTONIC" : compiles: YES (cached)
Checking whether type "struct tm" has member "tm_gmtoff" : NO (cached)
Checking whether type "struct tm" has member "__tm_gmtoff" : YES (cached)
Checking whether type "struct tm" has member "tm_sec" : YES (cached)
Checking whether type "struct tm" has member "tz_minuteswest" : NO (cached)
Checking for function "gettimeofday" : YES (cached)
Checking whether type "struct stat" has member "st_blocks" : YES (cached)
Checking for function "ioctl" : YES (cached)
Header <sys/ioctl.h> has symbol "TIOCGWINSZ" : YES (cached)
Header <sys/ioctl.h> has symbol "TIOCGETD" : YES (cached)
Checking for function "getpwuid" : YES (cached)
Checking for function "alarm" : YES (cached)
Checking for function "fcntl" : YES (cached)
Checking for function "flock" : YES (cached)
Checking for function "fork" : YES (cached)
Checking for function "frexpf" : YES (cached)
Checking for function "frexpl" : YES (cached)
Checking for function "gethostname" : YES (cached)
Checking for function "getrusage" : YES (cached)
Checking for function "llround" : YES (cached)
Checking for function "llroundf" : YES (cached)
Checking for function "lround" : YES (cached)
Checking for function "lroundf" : YES (cached)
Checking for function "lstat" : YES (cached)
Checking for function "pread" : YES (cached)
Checking for function "pwrite" : YES (cached)
Checking for function "rand_r" : YES (cached)
Checking for function "random" : YES (cached)
Checking for function "round" : YES (cached)
Checking for function "roundf" : YES (cached)
Checking for function "setsysinfo" : NO (cached)
Checking for function "signal" : YES (cached)
Checking for function "longjmp" : YES (cached)
Checking for function "setjmp" : YES (cached)
Checking for function "siglongjmp" : YES (cached)
Checking for function "sigsetjmp" : NO (cached)
Checking for function "sigprocmask" : YES (cached)
Checking for function "snprintf" : YES (cached)
Checking for function "srandom" : YES (cached)
Checking for function "strdup" : YES (cached)
Checking for function "strtoll" : YES (cached)
Checking for function "strtoull" : YES (cached)
Checking for function "symlink" : YES (cached)
Checking for function "system" : YES (cached)
Checking for function "tmpfile" : YES (cached)
Checking for function "asprintf" : YES (cached)
Checking for function "vasprintf" : YES (cached)
Checking for function "waitpid" : YES (cached)
Checking for function "vsnprintf" : YES (cached)
Header <setjmp.h> has symbol "sigsetjmp" : NO (cached)
Checking if "inline keyword check" : compiles: YES (cached)
Configuring H5pubconf.h using configuration
Checking for size of "long" : 8
Checking for size of "void *" : 8
Configuring cgnstypes.h using configuration
Configuring cg_hash_types.h using configuration
Configuring cgnsconfig.h using configuration
Compiler for C++ supports arguments -Wno-unused-result: YES (cached)
Compiler for C++ supports arguments -Wno-unused-parameter: YES (cached)
Compiler for C++ supports arguments -Wno-unused-variable: YES (cached)
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES (cached)
Compiler for C++ supports arguments -Wno-unknown-pragmas: YES (cached)
Compiler for C++ supports arguments -Wno-sign-compare: YES (cached)
Compiler for C++ supports arguments -Wno-clobbered: YES (cached)
Compiler for C++ supports arguments -Wno-empty-body: YES (cached)
Compiler for C++ supports arguments -Wno-unused-label: YES (cached)
Compiler for C++ supports arguments -Wno-misleading-indentation: YES (cached)
Compiler for C++ supports arguments -Wno-maybe-uninitialized: YES (cached)
Compiler for C++ supports arguments -Wno-pedantic: YES (cached)
Compiler for C++ supports arguments -Wno-error=absolute-value: YES (cached)
Compiler for C++ supports arguments -Wno-absolute-value: NO (cached)
WARNING: You should add the boolean check kwarg to the run_command call.
It currently defaults to false,
but it will default to true in future releases of meson.
See also: https://github.com/mesonbuild/meson/issues/9300
Message: Boost sources found.
Compiler for C++ supports arguments -Wno-misleading-indentation: YES (cached)
Compiler for C++ supports arguments -Wno-uninitialized: YES (cached)
Compiler for C++ supports arguments -Wno-placement-new: YES (cached)
Compiler for C++ supports arguments -Wno-pedantic: YES (cached)
Compiler for C++ supports arguments -Wno-error=class-memaccess: YES (cached)
Compiler for C++ supports arguments -Wno-class-memaccess: YES (cached)
Compiler for C++ supports arguments -Wno-error=deprecated-copy: YES (cached)
Compiler for C++ supports arguments -Wno-deprecated-copy: YES (cached)
Compiler for C++ supports arguments -Wno-error=cast-function-type: YES (cached)
Compiler for C++ supports arguments -Wno-cast-function-type: YES (cached)
Dependency mpich found: YES 4.0 (cached)
Message: -------------------------------------------------------------------------
| ___ _ _ ___ |
| / __| | | |_ ) Release 8.0.0 "Harrier" |
| \__ \ |_| |/ / |
| |___/\___//___| Meson Configuration Summary |
| |
-------------------------------------------------------------------------
Option Value
---------------------
TecIO: true
CGNS: true
AD (reverse): true
AD (forward): false
Python Wrapper: false
Intel-MKL: false
OpenBlas: false
PaStiX: false
Mixed Float: false
libROM: false
CoolProp: false
MLPCpp: false
Please be sure to add the $SU2_HOME and $SU2_RUN environment variables,
and update your $PATH (and $PYTHONPATH if applicable) with $SU2_RUN
Based on the input to this configuration, add these lines to your .bashrc file:
export SU2_RUN=/usr/local/bin
export SU2_HOME=/mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2
export PATH=$PATH:$SU2_RUN
export PYTHONPATH=$PYTHONPATH:$SU2_RUN
Use './ninja -C build install' to compile and install SU2
Build targets in project: 22
SU2 8.0.0 "Harrier"
User defined options
custom-mpi : true
enable-autodiff: true
extra-deps : mpich
with-mpi : enabled
Found ninja-1.10.0.git at /mnt/c/Users/muril/Documents/CFD/2023_11_SU2/new_turbo_outputs/su2/ninja
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November 25, 2023, 03:54
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I tried this but this gave me an error
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#6 | |
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New Member
Mohsin
Join Date: Jul 2023
Posts: 21
Rep Power: 3 |
Quote:
Code:
(base) mohsin@mohsin:~/Desktop/Constrained shape design of a transonic turbulent airfoil$ update-alternatives --config mpirun There are 2 choices for the alternative mpirun (providing /usr/bin/mpirun). Selection Path Priority Status ------------------------------------------------------------ * 0 /usr/bin/mpirun.openmpi 50 auto mode 1 /usr/bin/mpirun.mpich 40 manual mode 2 /usr/bin/mpirun.openmpi 50 manual mode Press <enter> to keep the current choice[*], or type selection number: 1 update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in manual mode update-alternatives: error: error creating symbolic link '/etc/alternatives/mpirun.dpkg-tmp': Permission denied |
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November 25, 2023, 04:05
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#7 |
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Senior Member
bigfoot
Join Date: Dec 2011
Location: Netherlands
Posts: 657
Rep Power: 19 |
update-alternatives should create symbolic links to cc with the right link to mpi. You can check with
Code:
which cc Code:
ls -lrt /usr/bin/cc You could force another default compiler by setting Code:
export MPICXX='/usr/bin/mpicxx.mpich' export MPICC='/usr/bin/mpicc.mpich' export CXX=$MPICXX export CC=$MPICC |
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November 25, 2023, 04:19
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#8 |
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Senior Member
bigfoot
Join Date: Dec 2011
Location: Netherlands
Posts: 657
Rep Power: 19 |
You can also test if mpi is correctly installed with a simple helloworld example, e.g.
Code:
#include <mpi.h>
#include <stdio.h>
int main(int argc, char** argv) {
// Initialize the MPI environment
MPI_Init(NULL, NULL);
// Get the number of processes
int world_size;
MPI_Comm_size(MPI_COMM_WORLD, &world_size);
// Get the rank of the process
int world_rank;
MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
// Get the name of the processor
char processor_name[MPI_MAX_PROCESSOR_NAME];
int name_len;
MPI_Get_processor_name(processor_name, &name_len);
// Print off a hello world message
printf("Hello world from processor %s, rank %d out of %d processors\n",
processor_name, world_rank, world_size);
// Finalize the MPI environment.
MPI_Finalize();
}
~
Code:
mpicc.mpich -o helloworld helloworld.c mpirun.mpich -n 4 ./helloworld |
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November 25, 2023, 04:46
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Thank you everyone for helping. I have solved the problem
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#9 |
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New Member
Mohsin
Join Date: Jul 2023
Posts: 21
Rep Power: 3 |
So, before I start explaining how i solved my problem, i would like to let you know that i am using following things:
ubuntu 22.04 (on virtual box version 7.0.10) anaconda3 python 3.11.4 SU2-7.5.1 1. I installed anaconda by using this command Code:
wget https://repo.anaconda.com/archive/Anaconda3-2023.07-2-Linux-x86_64.sh 3. Then i ran following commands one by one: Code:
conda install cmake conda install pkg-config conda install gxx_linux-64 pip install mpi4py pip install swig ./meson.py build -Dcustom-mpi=true -Dextra-deps=mpich -Denable-autodiff=true ./ninja -C build install Code:
nano .bashrc Code:
export SU2_RUN=/usr/local/bin export SU2_HOME=/home/mohsin/Downloads/SU2-7.5.1 export PATH=$PATH:$SU2_RUN export PYTHONPATH=$PYTHONPATH:$SU2_RUN Thats it. I am a newbie so i don't know why this worked but it worked lol |
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| Tags |
| cgns, mpi.h, mpich, parallel compilation, su2 |
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