[petsc-dev] Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process

Wed Oct 12 12:36:32 CDT 2016

On 10/12/2016 07:21 PM, Satish Balay wrote:
> On Wed, 12 Oct 2016, Antonio Trande wrote:
> 
>> On 10/11/2016 11:52 PM, Antonio Trande wrote:
>>> On 10/11/2016 09:39 PM, Satish Balay wrote:
>>>> On Tue, 11 Oct 2016, Antonio Trande wrote:
>>>>
>>>>> 'configure' does not recognize '-D_FORTIFY_SOURCE=2' flag (it says that
>>>>> should be -D-FORTIFY-SOURCE=2) that comes from default flags used on
>>>>> Fedora and automatically set when package is built. I'm forced to
>>>>> exclude it with 'configure' and re-introduce it with 'make'.
>>>>> This is the reason because flags are set more times.
>>>>> It's good if you can fix this problem with 'configure'.
>>>>
>>>> I suspect thats hapenning because you are missing quotes for CFLAGS=""
>>>> [as mentioned earlier] - so configure it treating -D_FORTIFY_SOURCE=2
>>>> as an argument to configure - and not as the text inside CFLAGS argument.
>>>>
>>>> Satish
>>>
>>> You're right.
>>> I'm fixing all settings of compiler flags.
>>>
>>
>> Is there a quick way to override compiler/linker flags in 'make test'?
>> I guess some flags could prevent running tests properly (there is no
>> errors when i use flags for debugging).
> 
> Its possible [by overriding stuff in PCC_FLAGS, PCC_LINKER_FLAGS etc -
> from PETSC_ARCH/lib/conf/petscvariables] But the error is comingfroma
> function in the petsc library [when it calls MPI] - so I'm not sure if
> that would make a difference.
> 
>>
>> Latest builds:
>> http://copr-fe.cloud.fedoraproject.org/coprs/sagitter/petsc/build/464373/
> 
> I've mentioned this a few times - You haven't been able to run the sequntial test in valgrind?

It was ran in valgrind:
https://copr-be.cloud.fedoraproject.org/results/sagitter/petsc/fedora-25-i386/00464297-petsc/build.log.gz

> 
> I'll try and see if I can reproduce this.. [in a 32bit VM]..
> 
> 
> Before doing further builds - perhaps you can clean up the configure options a bit more.
> https://copr-be.cloud.fedoraproject.org/results/sagitter/petsc/fedora-rawhide-i386/00464373-petsc/build.log.gz
> 
>>>>>>>>>>>
> 
> + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + COPTFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + CXXOPTFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + FOPTFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + export CFLAGS
> + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + export CXXFLAGS
> + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + export FFLAGS
> + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> + export FCFLAGS
> + LDFLAGS='-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
> + export LDFLAGS
> <<<<<<<<<<<
> 
> remove all these env flags. PETSc Configure does not process env flags..
> 
> 
> ./configure
> 
> --build=i686-redhat-linux-gnu
> --host=i686-redhat-linux-gnu
> --program-prefix=
> --disable-dependency-tracking
> --prefix=/usr
> --exec-prefix=/usr
> --bindir=/usr/bin
> --sbindir=/usr/sbin
> --sysconfdir=/etc
> --datadir=/usr/share
> --includedir=/usr/include
> --libdir=/usr/lib
> --libexecdir=/usr/libexec
> --localstatedir=/var
> --sharedstatedir=/var/lib
> --mandir=/usr/share/man
> --infodir=/usr/share/info
> 
> #[I understand some of the options are used by rpmbuild - which you can't eliminate]
> # Except for --prefix - none of the above options are used.
> 
> 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> 'FCFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> 'FFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> 'LDFLAGS=-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
> 'COPTFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> 'CXXOPTFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> 'FOPTFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables'
> 
> # I would remove duplicate options from COPTFLAGS, FOPTFLAGS CXXOPTFLAGS [they just make the compile lines longer - and harder to read. i.e specify them as: COPTFLAGS= FOPTFLAGS= CXXOPTFLAGS=
> 
> --with-default-arch=0
> --with-make=1
> --with-single-library=1
> --enable-shared=1
> 
> # --enable-shared is ignored - but --with-shared-libraries from below is used.
> 
> --with-precision=double
> --with-index-size=32
> 
> # --with-index-size is ignored

Okay; i will remove --enable-shared --with-index-size and all env flags.

> 
> --with-petsc-arch=i386
> --with-clanguage=C
> --with-shared-libraries=1
> --with-64-bit-indices=0
> --with-fortran-interfaces=1
> --with-windows-graphics=0
> --CC=gcc
> --FC=gfortran
> --with-gnu-compilers=1
> --with-vendor-compilers=0
> 
> # you are missing 'CXX=g++' - but then --with-gnu-compilers=1 is guessing and compensating. I would remove --with-gnu-compilers --with-vendor-compilers - and just list all compilers [CC, FC, CXX].
> 

g++ is not used, that's because i skipped it.
I will remove --with-gnu-compilers --with-vendor-compilers.

> --with-shared-ld=ld
> --with-pic=1
> --with-clib-autodetect=0
> --with-fortranlib-autodetect=0
> --with-threadsafety=0
> --with-log=1
> --with-cxxlib-autodetect=0
> --with-debugging=0
> '--with-blas-lapack-lib=-L/usr/lib -lopenblas'
> 
> # I would remove -L/usr/lib from everywhere..

This is another issue for me.
Lib list of Sundials is
'libsundials_cvode.a','libsundials_nvecserial.a','libsundials_nvecparallel.a']

If i'm not wrong, linking 'libsundials_nvecparallel.so' will require
'libsundials_cvode.so' but they are located in different directories
(/usr/lib/openmpi/lib and /usr/lib).

In this case, do i need using

--with-sundials-lib="-L/usr/lib -lsundials_cvode  -L/usr/lib/openmpi/lib
-lsundials_nvecparallel"

?

> 
> --known-64-bit-blas-indices=0
> --with-fc=gfortran
> 
> This is a duplicate for 'FC' - and would remove it. [i.e use CC, CXX, FC collectively - or use --with-cc, --with-cxx, --with-fc]

Okay.

> 
> --with-mpiuni-fortran-binding=1
> --with-mpi=0
> --with-x=1
> --with-openmp=0
> --with-metis=0
> --with-hwloc=0
> --with-ssl=0
> --with-pthread=1
> --with-valgrind=1
> 
> Satish
> 

-- 
---
Antonio Trande
mailto: sagitter 'at' fedoraproject 'dot' org
http://fedoraos.wordpress.com/
https://fedoraproject.org/wiki/User:Sagitter
GPG Key: 0x6CE6D08A
Check on https://keys.fedoraproject.org/

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