April 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] -with-kokkos-cuda-arch=AMPERE80 nonsense
by Scott Kruger 06 Apr '21

06 Apr '21

I wrote sent this yesterday but am having some strange mailing issues. On 2021-04-03 22:42, Barry Smith did write: > > It would be very nice to NOT require PETSc users to provide this flag, how the heck will they know what it should be when we cannot automate it ourselves? > > Any ideas of how this can be determined based on the current system? NVIDIA does not help since these "advertising" names don't seem to trivially map to information you can get from a particular GPU when you logged into it. For example nvidia-smi doesn't use these names directly. Is there some mapping from nvidia-smi to these names we could use? If we are serious about having a non-trivial number of users utilizing GPUs, which we need to be for future, we cannot have this absurd demands in our installation process. The mapping of the Nvidia card to the gencodes and cuda arch is one of those annoyances that is so ridiculous it is hard to believe. The best reference I have found is this: https://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvi… To this end, the fact that Kokkos provides a mapping from colloquial card name to gencode/arch is a real benefit and useful. The problem is that this mapping is buried in their build system and lacks introspection. > > Barry > > Does spack have some magic for this we could use? > spack developed the archspec repo to abstract all of these issues: https://github.com/archspec/archspec This is a *great* idea and eventually BuildSystem should incorporate it as the standard way of doing things; however, it is been focused mostly on the CPU issues, and is still under active development (my understanding is that the pulling it out of spack and getting those interop issues sorted out is tangled up in how spack handles dependencies and compilers). It'd be nice if someone would go in and port the Kokkos gpu mappings to archspec as there is some great knowledge on these mapping buried in the Kokkos build system (not volunteering); i.e., translating that webpage to some real code (even if it is in make) is valuable. TL;DR: It's a known problem with currently no good solution AFAIK. Waiting until archspec gets further along seems like the best solution. Scott P.S. ROCm has rocminfo which also doesn't solve the problem but is at least sane.

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Re: [petsc-dev] Petsc: Error code 1
by Barry Smith 06 Apr '21

06 Apr '21

> On Apr 6, 2021, at 12:06 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > >> See the attachements. alltest.log is on a machine with 96 cores, ARM, with FC,gcc9.3.5,mpich3.4.1,fblaslapack; 6 failures > > Perhaps this is an issue with ARM - and such diffs are expected - as we already have multiple alt files for some of these tests The function values are hugely different even at the beginning of the optimization which is why I don't think it is just round-off differences. > > $ ls -lt src/tao/bound/tutorials/output/plate2f_* > -rw-r--r--. 1 balay balay 1029 Mar 23 19:48 src/tao/bound/tutorials/output/plate2f_1_alt.out > -rw-r--r--. 1 balay balay 1071 Mar 23 19:48 src/tao/bound/tutorials/output/plate2f_1.out > -rw-r--r--. 1 balay balay 1029 Mar 23 19:48 src/tao/bound/tutorials/output/plate2f_2_alt.out > -rw-r--r--. 1 balay balay 1071 Mar 23 19:48 src/tao/bound/tutorials/output/plate2f_2.out > >>>>>>> > not ok diff-vec_is_is_tutorials-ex2f_1 # Error code: 1 > # 16,24d15 > # < 5 > # < 7 > # < 9 > # < 11 > # < 13 > # < 15 > # < 17 > # < 19 > # < 21 > <<<<< > > This one is puzzling - missing fortran stdout? Perhaps compile issue on ARM? [its a sequential example - so can't blame MPI] > > Or they are all related to the optimization flags used? What configure options were used for the build? > > Satish > > On Tue, 6 Apr 2021, Barry Smith wrote: > >> >> Alp, >> >> Except for the first test, these are all optimization problems (mostly in Fortran). The function values are very different so I am sending it to our optimization expert to take a look at it. The differences could possibly be related to the use of real() and maybe the direct use of floating point numbers that the compiler first treats as single and then converts to double thus losing precision. >> >> Chen Gang, I assume you compiled with the default standard precision PETSc configure options? >> >> >> >> On Apr 6, 2021, at 3:56 AM, Chen Gang <569615491(a)qq.com<mailto:[email protected]>> wrote: >> >> >> See the attachements. alltest.log is on a machine with 96 cores, ARM, with FC,gcc9.3.5,mpich3.4.1,fblaslapack; 6 failures >> alltest2.log is on an intel machine with 40 cores,x86, without FC; icc&mkl& intel mpi; only 1 failure >> >> ------------------ 原始邮件 ------------------ >> 发件人: "petsc-dev" <balay(a)mcs.anl.gov<mailto:[email protected]>>; >> 发送时间: 2021年4月6日(星期二) 中午12:38 >> 收件人: "petsc-dev"<petsc-dev(a)mcs.anl.gov<mailto:[email protected]>>; >> 抄送: "Chen Gang"<569615491(a)qq.com<mailto:[email protected]>>;"cglwdm"<cglwdm(a)scu.edu.cn<mailto:[email protected]>>; >> 主题: Re: [petsc-dev] Petsc: Error code 1 >> >> Note: do not use '-j' with alltests. >> >> And run alltests on both machines [but *not* at the same time on machines] and send us logs from both the runs. >> >> Satish >> >> >> On Mon, 5 Apr 2021, Satish Balay wrote: >> >>> Try: >>> >>> make alltests TIMEOUT=600 >>> >>> And send us the complete log (alltests.log) >>> >>> Satish >>> >>> On Tue, 6 Apr 2021, Chen Gang wrote: >>> >>>> Dear sir, >>>> >>>> >>>> The result of make check is OK. And I do set the timeout to a larger value, which keeps me from getting timeout error. The thing is I have two machines. And I get the error code 1 in different tests on different machines.I don’t know what is error code1. What case this? How can I fix the failure tests. >>>> >>>> >>>> ------------------ Original ------------------ >>>> From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> >>>> Date: Tue,Apr 6,2021 0:18 PM >>>> To: Chen Gang <569615491(a)qq.com<mailto:[email protected]>> >>>> Cc: petsc-dev <petsc-dev(a)mcs.anl.gov<mailto:[email protected]>>, cglwdm <cglwdm(a)scu.edu.cn<mailto:[email protected]>> >>>> Subject: Re: [petsc-dev] Petsc: Error code 1 >>> >> >> <alltests2.log><alltests.log> >>

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Re: [petsc-dev] Petsc: Error code 1
by Satish Balay 06 Apr '21

06 Apr '21

> See the attachements. alltest.log is on a machine with 96 cores, ARM, with FC,gcc9.3.5,mpich3.4.1,fblaslapack; 6 failures Perhaps this is an issue with ARM - and such diffs are expected - as we already have multiple alt files for some of these tests $ ls -lt src/tao/bound/tutorials/output/plate2f_* -rw-r--r--. 1 balay balay 1029 Mar 23 19:48 src/tao/bound/tutorials/output/plate2f_1_alt.out -rw-r--r--. 1 balay balay 1071 Mar 23 19:48 src/tao/bound/tutorials/output/plate2f_1.out -rw-r--r--. 1 balay balay 1029 Mar 23 19:48 src/tao/bound/tutorials/output/plate2f_2_alt.out -rw-r--r--. 1 balay balay 1071 Mar 23 19:48 src/tao/bound/tutorials/output/plate2f_2.out >>>>>> not ok diff-vec_is_is_tutorials-ex2f_1 # Error code: 1 # 16,24d15 # < 5 # < 7 # < 9 # < 11 # < 13 # < 15 # < 17 # < 19 # < 21 <<<<< This one is puzzling - missing fortran stdout? Perhaps compile issue on ARM? [its a sequential example - so can't blame MPI] Or they are all related to the optimization flags used? What configure options were used for the build? Satish On Tue, 6 Apr 2021, Barry Smith wrote: > > Alp, > > Except for the first test, these are all optimization problems (mostly in Fortran). The function values are very different so I am sending it to our optimization expert to take a look at it. The differences could possibly be related to the use of real() and maybe the direct use of floating point numbers that the compiler first treats as single and then converts to double thus losing precision. > > Chen Gang, I assume you compiled with the default standard precision PETSc configure options? > > > > On Apr 6, 2021, at 3:56 AM, Chen Gang <569615491(a)qq.com<mailto:[email protected]>> wrote: > > > See the attachements. alltest.log is on a machine with 96 cores, ARM, with FC,gcc9.3.5,mpich3.4.1,fblaslapack; 6 failures > alltest2.log is on an intel machine with 40 cores,x86, without FC; icc&mkl& intel mpi; only 1 failure > > ------------------ 原始锟绞硷拷 ------------------ > 锟斤拷锟斤拷锟斤拷: "petsc-dev" <balay(a)mcs.anl.gov<mailto:[email protected]>>; > 锟斤拷锟斤拷时锟斤拷: 2021锟斤拷4锟斤拷6锟斤拷(锟斤拷锟节讹拷) 锟斤拷锟斤拷12:38 > 锟秸硷拷锟斤拷: "petsc-dev"<petsc-dev(a)mcs.anl.gov<mailto:[email protected]>>; > 锟斤拷锟斤拷: "Chen Gang"<569615491(a)qq.com<mailto:[email protected]>>;"cglwdm"<cglwdm(a)scu.edu.cn<mailto:[email protected]>>; > 锟斤拷锟斤拷: Re: [petsc-dev] Petsc: Error code 1 > > Note: do not use '-j' with alltests. > > And run alltests on both machines [but *not* at the same time on machines] and send us logs from both the runs. > > Satish > > > On Mon, 5 Apr 2021, Satish Balay wrote: > > > Try: > > > > make alltests TIMEOUT=600 > > > > And send us the complete log (alltests.log) > > > > Satish > > > > On Tue, 6 Apr 2021, Chen Gang wrote: > > > > > Dear sir, > > > > > > > > > The result of make check is OK. And I do set the timeout to a larger value, which keeps me from getting timeout error. The thing is I have two machines. And I get the error code 1 in different tests on different machines.I don锟斤拷t know what is error code1. What case this? How can I fix the failure tests. > > > > > > > > > ------------------ Original ------------------ > > > From: Satish Balay <balay(a)mcs.anl.gov<mailto:[email protected]>> > > > Date: Tue,Apr 6,2021 0:18 PM > > > To: Chen Gang <569615491(a)qq.com<mailto:[email protected]>> > > > Cc: petsc-dev <petsc-dev(a)mcs.anl.gov<mailto:[email protected]>>, cglwdm <cglwdm(a)scu.edu.cn<mailto:[email protected]>> > > > Subject: Re: [petsc-dev] Petsc: Error code 1 > > > > <alltests2.log><alltests.log> > >

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Re: [petsc-dev] (arm64) could not find object file symbol for symbol ___muldc3
by Barry Smith 06 Apr '21

06 Apr '21

Blaise, Please send configure.log It would also be helpful if you could run nm -o /usr/lib/lib* | grep muldc3 Our cross language linker tests are not adding all the libraries they need to add when using Fortran for linking. Barry > On Apr 6, 2021, at 11:00 AM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Tue, Apr 6, 2021 at 11:04 AM Blaise A Bourdin <bourdin(a)lsu.edu <mailto:[email protected]>> wrote: > Hi, > > I am having the following warning when compiling any fortran example (currently on main, but it’s been going on for a little while) on a ARM mac. > > > *******************Error detected during compile or link!******************* > See http://www.mcs.anl.gov/petsc/documentation/faq.html <http://www.mcs.anl.gov/petsc/documentation/faq.html> > /opt/HPC/petsc-main/src/snes/tutorials ex5f > ********************************************************* > mpif90 -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -ffree-line-length-none -fallow-argument-mismatch -fPIC -g -ffree-line-length-none -fallow-argument-mismatch -fPIC -g -I/opt/HPC/petsc-main/include -I/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/include -I/opt/X11/include ex5f.F90 -Wl,-rpath,/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/lib -L/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/lib -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -Wl,-rpath,/opt/homebrew/Cellar/mpich/3.4.1_2/lib -L/opt/homebrew/Cellar/mpich/3.4.1_2/lib -Wl,-rpath,/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/aarch64-apple-darwin20/10.2.1 -L/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/aarch64-apple-darwin20/10.2.1 -Wl,-rpath,/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -llapack -lblas -lX11 -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lemutls_w -lm -lc++ -ldl -o ex5f > warning: (arm64) could not find object file symbol for symbol muldc3 > Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process > > > For reference, here is how I configured petsc: > ./configure --CFLAGS='-Wimplicit-function-declaration' --FFLAGS="-ffree-line-length-none -fallow-argument-mismatch" --with-debugging=1 --with-shared-libraries=1 --with-x11=1 > > It looks like this symbol is referenced in: sfpack.o > > SiMini:petsc-main (main)$ grep -ri muldc3 bigsur-gcc10.2-arm64-reallybasic-g/* > Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.3.015.0.dylib matches > Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.3.015.dylib matches > bigsur-gcc10.2-arm64-reallybasic-g/lib/petsc/conf/check.log:warning: (arm64) could not find object file symbol for symbol ___muldc3 > Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.dylib matches > Binary file bigsur-gcc10.2-arm64-reallybasic-g/obj/vec/is/sf/impls/basic/sfpack.o matches > > SiMini:petsc-main (main)$ nm bigsur-gcc10.2-arm64-reallybasic-g/obj/vec/is/sf/impls/basic/sfpack.o | grep muldc3 > U ___muldc3 > > Google tells me it is a gcc thing for complex multiplication. Ah, I think this is the problem: > > https://lists.mcs.anl.gov/pipermail/mpich-discuss/2012-August/012920.html <https://lists.mcs.anl.gov/pipermail/mpich-discuss/2012-August/012920.html> > > It is in the C library and you are linking from Fortran, so the compatibility libraries are not correct. > > Thanks, > > Matt > > Any idea? > Blaise > > > -- > A.K. & Shirley Barton Professor of Mathematics > Adjunct Professor of Mechanical Engineering > Adjunct of the Center for Computation & Technology > Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin <http://www.math.lsu.edu/~bourdin> > > > -- > What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Petsc: Error code 1
by Barry Smith 06 Apr '21

06 Apr '21

Alp, Except for the first test, these are all optimization problems (mostly in Fortran). The function values are very different so I am sending it to our optimization expert to take a look at it. The differences could possibly be related to the use of real() and maybe the direct use of floating point numbers that the compiler first treats as single and then converts to double thus losing precision. Chen Gang, I assume you compiled with the default standard precision PETSc configure options? > On Apr 6, 2021, at 3:56 AM, Chen Gang <569615491(a)qq.com> wrote: > > > See the attachements. alltest.log is on a machine with 96 cores, ARM, with FC,gcc9.3.5,mpich3.4.1,fblaslapack; 6 failures > alltest2.log is on an intel machine with 40 cores,x86, without FC; icc&mkl& intel mpi; only 1 failure > > ------------------ 原始邮件 ------------------ > 发件人: "petsc-dev" <balay(a)mcs.anl.gov>; > 发送时间: 2021年4月6日(星期二) 中午12:38 > 收件人: "petsc-dev"<petsc-dev(a)mcs.anl.gov>; > 抄送: "Chen Gang"<569615491(a)qq.com>;"cglwdm"<cglwdm(a)scu.edu.cn>; > 主题: Re: [petsc-dev] Petsc: Error code 1 > > Note: do not use '-j' with alltests. > > And run alltests on both machines [but *not* at the same time on machines] and send us logs from both the runs. > > Satish > > > On Mon, 5 Apr 2021, Satish Balay wrote: > > > Try: > > > > make alltests TIMEOUT=600 > > > > And send us the complete log (alltests.log) > > > > Satish > > > > On Tue, 6 Apr 2021, Chen Gang wrote: > > > > > Dear sir, > > > > > > > > > The result of make check is OK. And I do set the timeout to a larger value, which keeps me from getting timeout error. The thing is I have two machines. And I get the error code 1 in different tests on different machines.I don’t know what is error code1. What case this? How can I fix the failure tests. > > > > > > > > > ------------------ Original ------------------ > > > From: Satish Balay <balay(a)mcs.anl.gov> > > > Date: Tue,Apr 6,2021 0:18 PM > > > To: Chen Gang <569615491(a)qq.com> > > > Cc: petsc-dev <petsc-dev(a)mcs.anl.gov>, cglwdm <cglwdm(a)scu.edu.cn> > > > Subject: Re: [petsc-dev] Petsc: Error code 1 > > > > <alltests2.log><alltests.log>

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Re: [petsc-dev] Petsc: Error code 1 TS adapt difference
by Barry Smith 06 Apr '21

06 Apr '21

Emil and Hong, In this test the GLEE time step adapter is making a different decision on accepting or rejecting a step. It could be due to slight differences in round-off for different machines and compilers. I leave it to our ODE experts to take a look at it. Barry > On Apr 6, 2021, at 3:56 AM, Chen Gang <569615491(a)qq.com> wrote: > > > See the attachements. alltest.log is on a machine with 96 cores, ARM, with FC,gcc9.3.5,mpich3.4.1,fblaslapack; 6 failures > alltest2.log is on an intel machine with 40 cores,x86, without FC; icc&mkl& intel mpi; only 1 failure > > ------------------ 原始邮件 ------------------ > 发件人: "petsc-dev" <balay(a)mcs.anl.gov>; > 发送时间: 2021年4月6日(星期二) 中午12:38 > 收件人: "petsc-dev"<petsc-dev(a)mcs.anl.gov>; > 抄送: "Chen Gang"<569615491(a)qq.com>;"cglwdm"<cglwdm(a)scu.edu.cn>; > 主题: Re: [petsc-dev] Petsc: Error code 1 > > Note: do not use '-j' with alltests. > > And run alltests on both machines [but *not* at the same time on machines] and send us logs from both the runs. > > Satish > > > On Mon, 5 Apr 2021, Satish Balay wrote: > > > Try: > > > > make alltests TIMEOUT=600 > > > > And send us the complete log (alltests.log) > > > > Satish > > > > On Tue, 6 Apr 2021, Chen Gang wrote: > > > > > Dear sir, > > > > > > > > > The result of make check is OK. And I do set the timeout to a larger value, which keeps me from getting timeout error. The thing is I have two machines. And I get the error code 1 in different tests on different machines.I don’t know what is error code1. What case this? How can I fix the failure tests. > > > > > > > > > ------------------ Original ------------------ > > > From: Satish Balay <balay(a)mcs.anl.gov> > > > Date: Tue,Apr 6,2021 0:18 PM > > > To: Chen Gang <569615491(a)qq.com> > > > Cc: petsc-dev <petsc-dev(a)mcs.anl.gov>, cglwdm <cglwdm(a)scu.edu.cn> > > > Subject: Re: [petsc-dev] Petsc: Error code 1 > > > > <alltests2.log><alltests.log>

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Re: [petsc-dev] -with-kokkos-cuda-arch=AMPERE80 nonsense
by Barry Smith 06 Apr '21

06 Apr '21

Jeff, Likely deviceQuery provides more than enough information; sometimes it is prebuilt but it seems now it is only provided as source code so the user needs to build it (and the Makefile is huge :-)). I think it would be enough if NVIDIA just always provided prebuilt deviceQuery in a standard location. Barry > On Apr 6, 2021, at 12:42 AM, Jeff Hammond <jeff.science(a)gmail.com> wrote: > > > Generically, independent of Kokkos, ideally I would run a single precompiled NVIDIA program that gave me all the information about the current hardware I was running and that would provide in simple format exactly the information I needed to configure PETSc, Kokkos etc for THAT system. > > I will try to write something for you tomorrow. For NVIDIA hardware, the sole dependency will be nvcc. > > Jeff > > -- > Jeff Hammond > jeff.science(a)gmail.com <mailto:[email protected]> > http://jeffhammond.github.io/ <http://jeffhammond.github.io/>

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Re: [petsc-dev] (arm64) could not find object file symbol for symbol ___muldc3
by Matthew Knepley 06 Apr '21

06 Apr '21

On Tue, Apr 6, 2021 at 11:04 AM Blaise A Bourdin <bourdin(a)lsu.edu> wrote: > Hi, > > I am having the following warning when compiling any fortran example > (currently on main, but it’s been going on for a little while) on a ARM > mac. > > > *******************Error detected during compile or > link!******************* > See http://www.mcs.anl.gov/petsc/documentation/faq.html > /opt/HPC/petsc-main/src/snes/tutorials ex5f > ********************************************************* > mpif90 -Wl,-bind_at_load -Wl,-multiply_defined,suppress > -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs > -Wl,-search_paths_first -Wl,-no_compact_unwind -ffree-line-length-none > -fallow-argument-mismatch -fPIC -g -ffree-line-length-none > -fallow-argument-mismatch -fPIC -g -I/opt/HPC/petsc-main/include > -I/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/include > -I/opt/X11/include ex5f.F90 > -Wl,-rpath,/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/lib > -L/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/lib > -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib > -Wl,-rpath,/opt/homebrew/Cellar/mpich/3.4.1_2/lib > -L/opt/homebrew/Cellar/mpich/3.4.1_2/lib > -Wl,-rpath,/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/aarch64-apple-darwin20/10.2.1 > -L/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/aarch64-apple-darwin20/10.2.1 > -Wl,-rpath,/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10 > -lpetsc -llapack -lblas -lX11 -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran > -lemutls_w -lm -lc++ -ldl -o ex5f > warning: (arm64) could not find object file symbol for symbol muldc3 > Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process > > > For reference, here is how I configured petsc: > ./configure --CFLAGS='-Wimplicit-function-declaration' > --FFLAGS="-ffree-line-length-none -fallow-argument-mismatch" > --with-debugging=1 --with-shared-libraries=1 > --with-x11=1 > > It looks like this symbol is referenced in: sfpack.o > > *SiMini*:petsc-main (main)$ grep -ri muldc3 > bigsur-gcc10.2-arm64-reallybasic-g/* > Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.3.015.0.dylib > matches > Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.3.015.dylib > matches > bigsur-gcc10.2-arm64-reallybasic-g/lib/petsc/conf/check.log:warning: > (arm64) could not find object file symbol for symbol ___muldc3 > Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.dylib matches > Binary file > bigsur-gcc10.2-arm64-reallybasic-g/obj/vec/is/sf/impls/basic/sfpack.o > matches > > *SiMini*:petsc-main (main)$ nm > bigsur-gcc10.2-arm64-reallybasic-g/obj/vec/is/sf/impls/basic/sfpack.o | > grep muldc3 > U ___muldc3 > Google tells me it is a gcc thing for complex multiplication. Ah, I think this is the problem: https://lists.mcs.anl.gov/pipermail/mpich-discuss/2012-August/012920.html It is in the C library and you are linking from Fortran, so the compatibility libraries are not correct. Thanks, Matt > Any idea? > Blaise > > > -- > A.K. & Shirley Barton Professor of Mathematics > Adjunct Professor of Mechanical Engineering > Adjunct of the Center for Computation & Technology > Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, > USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web > http://www.math.lsu.edu/~bourdin > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] Regression in manualpages generation?
by Pierre Jolivet 06 Apr '21

06 Apr '21

> On 6 Apr 2021, at 5:03 PM, Satish Balay <balay(a)mcs.anl.gov> wrote: > > > https://www.mcs.anl.gov/petsc/petsc-current/ is from petsc-3.15.0 - > and is normally gets updated with the next patch release - i.e > petsc-3.15.1. [ok - I'll update now with current release snapshot] Ah, of course, I don’t know why I checked there instead of the dev version, my bad. Well, thank you for updating the 3.15.0 pages as well I guess. Thanks, Pierre > Also dev pages should get updated daily [there is a bug here > that I should fix] > > With the latest snapshots - both the pages appear to list MatGetRow_MPIDense > > https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetRow.… > https://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/Mat/MatGetRow.html > > Satish > > On Tue, 6 Apr 2021, Pierre Jolivet wrote: > >> Thanks for the recent MR. >> This sadly only partially addresses the issue. >> https://www.mcs.anl.gov/petsc/petsc-3.14.6/docs/manualpages/Mat/MatGetRow.h… <https://www.mcs.anl.gov/petsc/petsc-3.14.6/docs/manualpages/Mat/MatGetRow.h…> correctly has MatGetRow_MPIDense while https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetRow.… <https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatGetRow.…> hasn’t. >> >> Thanks, >> Pierre >> >>> On 3 Apr 2021, at 1:24 PM, Patrick Sanan <patrick.sanan(a)gmail.com> wrote: >>> >>> I think this was likely a non-portable regex that was being used to match the function signatures, >>> causing it to miss anything with an internal "s" in the function name. Here's a quick fix for the release branch: >>> >>> https://gitlab.com/petsc/petsc/-/merge_requests/3813 <https://gitlab.com/petsc/petsc/-/merge_requests/3813> >>> >>> (This sort of thing will become easier to work with, soon, as we'll have an automated doc build which can be examined for each MR.) >>> >>> P.S. nice email address! >>> >>>> Am 03.04.2021 um 11:19 schrieb Patrick Sanan <patrick.sanan(a)gmail.com <mailto:[email protected]>>: >>>> >>>> That isn't expected - thanks for pointing this out! I can reproduce locally so will take a look. >>>> >>>>> Am 03.04.2021 um 11:10 schrieb Pierre Jolivet <pierre(a)joliv.et <mailto:[email protected]>>: >>>>> >>>>> Hello, >>>>> https://www.mcs.anl.gov/petsc/petsc-3.14/docs/manualpages/Mat/MatTranspose.… <https://www.mcs.anl.gov/petsc/petsc-3.14/docs/manualpages/Mat/MatTranspose.…> lists available implementations while https://www.mcs.anl.gov/petsc/petsc-3.15/docs/manualpages/Mat/MatTranspose.… <https://www.mcs.anl.gov/petsc/petsc-3.15/docs/manualpages/Mat/MatTranspose.…> doesn’t. >>>>> Is this expected? >>>>> >>>>> Thanks, >>>>> Pierre >>>> >>> >> >>

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(arm64) could not find object file symbol for symbol ___muldc3
by Blaise A Bourdin 06 Apr '21

06 Apr '21

Hi, I am having the following warning when compiling any fortran example (currently on main, but it’s been going on for a little while) on a ARM mac. *******************Error detected during compile or link!******************* See http://www.mcs.anl.gov/petsc/documentation/faq.html /opt/HPC/petsc-main/src/snes/tutorials ex5f ********************************************************* mpif90 -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind -ffree-line-length-none -fallow-argument-mismatch -fPIC -g -ffree-line-length-none -fallow-argument-mismatch -fPIC -g -I/opt/HPC/petsc-main/include -I/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/include -I/opt/X11/include ex5f.F90 -Wl,-rpath,/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/lib -L/opt/HPC/petsc-main/bigsur-gcc10.2-arm64-reallybasic-g/lib -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -Wl,-rpath,/opt/homebrew/Cellar/mpich/3.4.1_2/lib -L/opt/homebrew/Cellar/mpich/3.4.1_2/lib -Wl,-rpath,/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/aarch64-apple-darwin20/10.2.1 -L/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10/gcc/aarch64-apple-darwin20/10.2.1 -Wl,-rpath,/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10 -L/opt/homebrew/Cellar/gcc/10.2.0_4/lib/gcc/10 -lpetsc -llapack -lblas -lX11 -lc++ -ldl -lmpifort -lmpi -lpmpi -lgfortran -lemutls_w -lm -lc++ -ldl -o ex5f warning: (arm64) could not find object file symbol for symbol ___muldc3 Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process For reference, here is how I configured petsc: ./configure --CFLAGS='-Wimplicit-function-declaration' --FFLAGS="-ffree-line-length-none -fallow-argument-mismatch" --with-debugging=1 --with-shared-libraries=1 --with-x11=1 It looks like this symbol is referenced in: sfpack.o SiMini:petsc-main (main)$ grep -ri muldc3 bigsur-gcc10.2-arm64-reallybasic-g/* Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.3.015.0.dylib matches Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.3.015.dylib matches bigsur-gcc10.2-arm64-reallybasic-g/lib/petsc/conf/check.log:warning: (arm64) could not find object file symbol for symbol ___muldc3 Binary file bigsur-gcc10.2-arm64-reallybasic-g/lib/libpetsc.dylib matches Binary file bigsur-gcc10.2-arm64-reallybasic-g/obj/vec/is/sf/impls/basic/sfpack.o matches SiMini:petsc-main (main)$ nm bigsur-gcc10.2-arm64-reallybasic-g/obj/vec/is/sf/impls/basic/sfpack.o | grep muldc3 U ___muldc3 Any idea? Blaise -- A.K. & Shirley Barton Professor of Mathematics Adjunct Professor of Mechanical Engineering Adjunct of the Center for Computation & Technology Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin

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