[Llvm-bgq-discuss] clang fatal error compiling GROMACS for BlueGene/Q

Sun Sep 29 15:16:36 CDT 2013

----- Original Message -----
> 
> -O2 and -O3 both crashed the same way on nb_kernel_ref.c, but -O1
> succeeded.
> 
> -O1 crashed on three other files, though :-(

I think that -O1 is the most-lightly tested optimization option in general. ;)

> 
> 
> To be fair, I'm being evil and using OpenMP, so I should probably
> desist from that!

I'd like you to test the OpenMP, but you may want to test both ways for now because the OpenMP support is still in its very early days.

Thanks again,
Hal

> 
> 
> .c and .sh files:
> 
> 
> https://docs.google.com/file/d/0B0H2SbsMc3_qVVdwVVphQ0wzazg/edit?usp=sharing
> https://docs.google.com/file/d/0B0H2SbsMc3_qVXRMUUVTX2tNQ1E/edit?usp=sharing
> https://docs.google.com/file/d/0B0H2SbsMc3_qZHZxLXlydEl4cUU/edit?usp=sharing
> https://docs.google.com/file/d/0B0H2SbsMc3_qZVVpMGlWYU1aWVk/edit?usp=sharing
> https://docs.google.com/file/d/0B0H2SbsMc3_qbGFCX29fRVRSX2s/edit?usp=sharing
> https://docs.google.com/file/d/0B0H2SbsMc3_qeEJhMUcxTnFSWTg/edit?usp=sharing
> 
> Stack traces follow
> 
> clang:
> /gpfs/vesta-home/hfinkel/rpmbuild/BUILD/llvm/include/llvm/IR/Instructions.h:2131:
> llvm::Value* llvm::PHINode::removeIncomingValue(const
> llvm::BasicBlock*, bool): Assertion `Idx >= 0 && "Invalid basic
> block argument to remove!"' failed.
> 0 libLLVM-3.4svn.so 0x00000fff800d4a9c
> llvm::sys::PrintStackTrace(_IO_FILE*) + 4281424836
> 1 libLLVM-3.4svn.so 0x00000fff800d4d00
> 2 libLLVM-3.4svn.so 0x00000fff800d5ba4
> 3 0x00000fff80e20418 __kernel_sigtramp_rt64 + 0
> 4 libc.so.6 0x00000080c3766ef8 abort + 4293479848
> 5 libc.so.6 0x00000080c375b98c
> 6 libc.so.6 0x00000080c375baa4 __assert_fail + 4293437492
> 7 libLLVM-3.4svn.so 0x00000fff801553e4
> 8 libLLVM-3.4svn.so 0x00000fff80155948
> llvm::SplitBlockPredecessors(llvm::BasicBlock*,
> llvm::ArrayRef<llvm::BasicBlock*>, char const*, llvm::Pass*) +
> 4281935200
> 9 libLLVM-3.4svn.so 0x00000fff80182f74
> llvm::InsertPreheaderForLoop(llvm::Loop*, llvm::Pass*) + 4282118220
> 10 libLLVM-3.4svn.so 0x00000fff801862b8
> 11 libLLVM-3.4svn.so 0x00000fff7f44227c
> llvm::LPPassManager::runOnFunction(llvm::Function&) + 4268565020
> 12 libLLVM-3.4svn.so 0x00000fff7f8f29b8
> llvm::FPPassManager::runOnFunction(llvm::Function&) + 4273352968
> 13 libLLVM-3.4svn.so 0x00000fff7f8f2afc
> llvm::FPPassManager::runOnModule(llvm::Module&) + 4273353276
> 14 libLLVM-3.4svn.so 0x00000fff7f8f22bc
> llvm::MPPassManager::runOnModule(llvm::Module&) + 4273351228
> 15 libLLVM-3.4svn.so 0x00000fff7f8f25e4
> llvm::PassManagerImpl::run(llvm::Module&) + 4273352020
> 16 libLLVM-3.4svn.so 0x00000fff7f8f26f4
> llvm::PassManager::run(llvm::Module&) + 4273352276
> 17 clang 0x00000000103ae874
> 18 clang 0x00000000103af7f8
> clang::EmitBackendOutput(clang::DiagnosticsEngine&,
> clang::CodeGenOptions const&, clang::TargetOptions const&,
> clang::LangOptions const&, llvm::Module*, clang::BackendAction,
> llvm::raw_ostream*) + 4272665128
> 19 clang 0x00000000103ab4a4
> 20 clang 0x000000001059f230 clang::ParseAST(clang::Sema&, bool, bool)
> + 4274649152
> 21 clang 0x00000000101e4b64 clang::ASTFrontendAction::ExecuteAction()
> + 4270836484
> 22 clang 0x00000000103a9b00 clang::CodeGenAction::ExecuteAction() +
> 4272641808
> 23 clang 0x00000000101e4fb4 clang::FrontendAction::Execute() +
> 4270837524
> 24 clang 0x00000000101be154
> clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) +
> 4270679924
> 25 clang 0x000000001019f894
> clang::ExecuteCompilerInvocation(clang::CompilerInstance*) +
> 4270560804
> 26 clang 0x00000000101959d8 cc1_main(char const**, char const**, char
> const*, void*) + 4270520648
> 27 clang 0x000000001019d540 main + 4270551792
> 28 libc.so.6 0x00000080c374bcf8
> 29 libc.so.6 0x00000080c374bef0 __libc_start_main + 4293374496
> Stack dump:
> 0. Program arguments:
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/clang
> -cc1 -fopenmp -triple powerpc64-bgq-linux -S -disable-free
> -main-file-name calch.c -static-define -mrelocation-model static
> -mdisable-fp-elim -ffp-contract=fast -mconstructor-aliases
> -target-cpu a2q -target-linker-version 2.20.51.0.2 -coverage-file
> /tmp/calch-6bbf4d.s -resource-dir
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/../lib/clang/3.4
> -D __bgclang__=1 -D __bgclang_version__="r000000-00000000" -D
> HAVE_CONFIG_H -D TMPI_EXPORTS -D NDEBUG -I
> /bgsys/local/clang/llvm.r190771/r190771-20130914/sleef/include -I
> /bgsys/local/clang/llvm.r190771/r190771-20130914/omp/include -I
> /bgsys/drivers/V1R2M1/ppc64/comm/include -I
> /bgsys/drivers/V1R2M1/ppc64/comm/lib/gnu -I
> /bgsys/drivers/V1R2M1/ppc64 -I
> /bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I
> /bgsys/drivers/V1R2M1/ppc64/spi/include -I
> /bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/src
> -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/include
> -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/include
> -I /homeb/zdv518/zdv518/progs/bgsys-clang/include -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/src/gmxlib
> -I /bgsys/drivers/V1R2M1/ppc64/comm/include -internal-isystem
> /usr/local/include -internal-isystem
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/../lib/clang/3.4/include
> -internal-externc-isystem /include -internal-externc-isystem
> /usr/include -O1 -Wall -Wno-unused -Wunused-value
> -fno-dwarf-directory-asm -fdebug-compilation-dir
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/src/gmxlib
> -ferror-limit 19 -fmessage-length 108 -mstackrealign
> -fno-signed-char -fobjc-runtime=gcc
> -fobjc-default-synthesize-properties -fdiagnostics-show-option
> -fcolor-diagnostics -vectorize-slp -isystem
> /bgsys/drivers/V1R2M1/ppc64/gnu-linux/powerpc64-bgq-linux/sys-include
> -mllvm -optimize-regalloc -mllvm -fast-isel=0 -o /tmp/calch-6bbf4d.s
> -x c
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/src/gmxlib/calch.c
> 1. <eof> parser at end of file
> 2. Code generation
> 3. Running pass 'Function Pass Manager' on module
> '/homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/src/gmxlib/calch.c'.
> 4. Running pass 'Loop Pass Manager' on function '@calc_h_pos'
> 5. Running pass 'Canonicalize natural loops' on basic block
> '%for.body'
> clang: error: unable to execute command: Aborted (core dumped)
> clang: error: clang frontend command failed due to signal (use -v to
> see invocation)
> clang version 3.4 (trunk)
> Target: powerpc64-bgq-linux
> Thread model: posix
> clang: note: diagnostic msg: PLEASE submit a bug report to
> http://llvm.org/bugs/ and include the crash backtrace, preprocessed
> source, and associated run script.
> clang: note: diagnostic msg:
> ********************
> 
> PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
> Preprocessed source(s) and associated run script(s) are located at:
> clang: note: diagnostic msg: /tmp/calch-6d5809.c
> clang: note: diagnostic msg: /tmp/calch-6d5809.sh
> clang: note: diagnostic msg:
> 
> 
> NEXT STACK TRACE
> 
> clang:
> /gpfs/vesta-home/hfinkel/rpmbuild/BUILD/llvm/include/llvm/IR/Instructions.h:2131:
> llvm::Value* llvm::PHINode::removeIncomingValue(const
> llvm::BasicBlock*, bool): Assertion `Idx >= 0 && "Invalid basic
> block argument to remove!"' failed.
> 0 libLLVM-3.4svn.so 0x00000fff7ccb4a9c
> llvm::sys::PrintStackTrace(_IO_FILE*) + 4281424836
> 1 libLLVM-3.4svn.so 0x00000fff7ccb4d00
> 2 libLLVM-3.4svn.so 0x00000fff7ccb5ba4
> 3 0x00000fff7da00418 __kernel_sigtramp_rt64 + 0
> 4 libc.so.6 0x00000080c3766ef8 abort + 4293479848
> 5 libc.so.6 0x00000080c375b98c
> 6 libc.so.6 0x00000080c375baa4 __assert_fail + 4293437492
> 7 libLLVM-3.4svn.so 0x00000fff7cd353e4
> 8 libLLVM-3.4svn.so 0x00000fff7cd35948
> llvm::SplitBlockPredecessors(llvm::BasicBlock*,
> llvm::ArrayRef<llvm::BasicBlock*>, char const*, llvm::Pass*) +
> 4281935200
> 9 libLLVM-3.4svn.so 0x00000fff7cd62f74
> llvm::InsertPreheaderForLoop(llvm::Loop*, llvm::Pass*) + 4282118220
> 10 libLLVM-3.4svn.so 0x00000fff7cd662b8
> 11 libLLVM-3.4svn.so 0x00000fff7c02227c
> llvm::LPPassManager::runOnFunction(llvm::Function&) + 4268565020
> 12 libLLVM-3.4svn.so 0x00000fff7c4d29b8
> llvm::FPPassManager::runOnFunction(llvm::Function&) + 4273352968
> 13 libLLVM-3.4svn.so 0x00000fff7c4d2afc
> llvm::FPPassManager::runOnModule(llvm::Module&) + 4273353276
> 14 libLLVM-3.4svn.so 0x00000fff7c4d22bc
> llvm::MPPassManager::runOnModule(llvm::Module&) + 4273351228
> 15 libLLVM-3.4svn.so 0x00000fff7c4d25e4
> llvm::PassManagerImpl::run(llvm::Module&) + 4273352020
> 16 libLLVM-3.4svn.so 0x00000fff7c4d26f4
> llvm::PassManager::run(llvm::Module&) + 4273352276
> 17 clang 0x00000000103ae874
> 18 clang 0x00000000103af7f8
> clang::EmitBackendOutput(clang::DiagnosticsEngine&,
> clang::CodeGenOptions const&, clang::TargetOptions const&,
> clang::LangOptions const&, llvm::Module*, clang::BackendAction,
> llvm::raw_ostream*) + 4272665128
> 19 clang 0x00000000103ab4a4
> 20 clang 0x000000001059f230 clang::ParseAST(clang::Sema&, bool, bool)
> + 4274649152
> 21 clang 0x00000000101e4b64 clang::ASTFrontendAction::ExecuteAction()
> + 4270836484
> 22 clang 0x00000000103a9b00 clang::CodeGenAction::ExecuteAction() +
> 4272641808
> 23 clang 0x00000000101e4fb4 clang::FrontendAction::Execute() +
> 4270837524
> 24 clang 0x00000000101be154
> clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) +
> 4270679924
> 25 clang 0x000000001019f894
> clang::ExecuteCompilerInvocation(clang::CompilerInstance*) +
> 4270560804
> 26 clang 0x00000000101959d8 cc1_main(char const**, char const**, char
> const*, void*) + 4270520648
> 27 clang 0x000000001019d540 main + 4270551792
> 28 libc.so.6 0x00000080c374bcf8
> 29 libc.so.6 0x00000080c374bef0 __libc_start_main + 4293374496
> Stack dump:
> 0. Program arguments:
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/clang
> -cc1 -fopenmp -triple powerpc64-bgq-linux -S -disable-free
> -main-file-name pull.c -static-define -mrelocation-model static
> -mdisable-fp-elim -ffp-contract=fast -mconstructor-aliases
> -target-cpu a2q -target-linker-version 2.20.51.0.2 -coverage-file
> /tmp/pull-534714.s -resource-dir
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/../lib/clang/3.4
> -D __bgclang__=1 -D __bgclang_version__="r000000-00000000" -D
> HAVE_CONFIG_H -D NDEBUG -I
> /bgsys/local/clang/llvm.r190771/r190771-20130914/sleef/include -I
> /bgsys/local/clang/llvm.r190771/r190771-20130914/omp/include -I
> /bgsys/drivers/V1R2M1/ppc64/comm/include -I
> /bgsys/drivers/V1R2M1/ppc64/comm/lib/gnu -I
> /bgsys/drivers/V1R2M1/ppc64 -I
> /bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I
> /bgsys/drivers/V1R2M1/ppc64/spi/include -I
> /bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/src
> -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/include
> -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/include
> -I /homeb/zdv518/zdv518/progs/bgsys-clang/include -I
> /bgsys/drivers/V1R2M1/ppc64/comm/include -internal-isystem
> /usr/local/include -internal-isystem
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/../lib/clang/3.4/include
> -internal-externc-isystem /include -internal-externc-isystem
> /usr/include -O1 -Wall -Wno-unused -Wunused-value
> -fno-dwarf-directory-asm -fdebug-compilation-dir
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/src/mdlib
> -ferror-limit 19 -fmessage-length 277 -mstackrealign
> -fno-signed-char -fobjc-runtime=gcc
> -fobjc-default-synthesize-properties -fdiagnostics-show-option
> -fcolor-diagnostics -vectorize-slp -isystem
> /bgsys/drivers/V1R2M1/ppc64/gnu-linux/powerpc64-bgq-linux/sys-include
> -mllvm -optimize-regalloc -mllvm -fast-isel=0 -o /tmp/pull-534714.s
> -x c
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/src/mdlib/pull.c
> 1. <eof> parser at end of file
> 2. Code generation
> 3. Running pass 'Function Pass Manager' on module
> '/homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/src/mdlib/pull.c'.
> 4. Running pass 'Loop Pass Manager' on function
> '@get_pullgrp_distance'
> 5. Running pass 'Canonicalize natural loops' on basic block
> '%for.body39'
> clang: error: unable to execute command: Aborted (core dumped)
> clang: error: clang frontend command failed due to signal (use -v to
> see invocation)
> clang version 3.4 (trunk)
> Target: powerpc64-bgq-linux
> Thread model: posix
> clang: note: diagnostic msg: PLEASE submit a bug report to
> http://llvm.org/bugs/ and include the crash backtrace, preprocessed
> source, and associated run script.
> clang: note: diagnostic msg:
> ********************
> 
> PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
> Preprocessed source(s) and associated run script(s) are located at:
> clang: note: diagnostic msg: /tmp/pull-39d5bc.c
> clang: note: diagnostic msg: /tmp/pull-39d5bc.sh
> clang: note: diagnostic msg:
> 
> ********************
> 
> 
> NEXT STACK TRACE
> 
> 
> clang:
> /gpfs/vesta-home/hfinkel/rpmbuild/BUILD/llvm/include/llvm/IR/Instructions.h:2131:
> llvm::Value* llvm::PHINode::removeIncomingValue(const
> llvm::BasicBlock*, bool): Assertion `Idx >= 0 && "Invalid basic
> block argument to remove!"' failed.
> 0 libLLVM-3.4svn.so 0x00000fff91fd4a9c
> llvm::sys::PrintStackTrace(_IO_FILE*) + 4281424836
> 1 libLLVM-3.4svn.so 0x00000fff91fd4d00
> 2 libLLVM-3.4svn.so 0x00000fff91fd5ba4
> 3 0x00000fff92d20418 __kernel_sigtramp_rt64 + 0
> 4 libc.so.6 0x00000080c3766ef8 abort + 4293479848
> 5 libc.so.6 0x00000080c375b98c
> 6 libc.so.6 0x00000080c375baa4 __assert_fail + 4293437492
> 7 libLLVM-3.4svn.so 0x00000fff920553e4
> 8 libLLVM-3.4svn.so 0x00000fff92055948
> llvm::SplitBlockPredecessors(llvm::BasicBlock*,
> llvm::ArrayRef<llvm::BasicBlock*>, char const*, llvm::Pass*) +
> 4281935200
> 9 libLLVM-3.4svn.so 0x00000fff92082f74
> llvm::InsertPreheaderForLoop(llvm::Loop*, llvm::Pass*) + 4282118220
> 10 libLLVM-3.4svn.so 0x00000fff920862b8
> 11 libLLVM-3.4svn.so 0x00000fff9134227c
> llvm::LPPassManager::runOnFunction(llvm::Function&) + 4268565020
> 12 libLLVM-3.4svn.so 0x00000fff917f29b8
> llvm::FPPassManager::runOnFunction(llvm::Function&) + 4273352968
> 13 libLLVM-3.4svn.so 0x00000fff917f2afc
> llvm::FPPassManager::runOnModule(llvm::Module&) + 4273353276
> 14 libLLVM-3.4svn.so 0x00000fff917f22bc
> llvm::MPPassManager::runOnModule(llvm::Module&) + 4273351228
> 15 libLLVM-3.4svn.so 0x00000fff917f25e4
> llvm::PassManagerImpl::run(llvm::Module&) + 4273352020
> 16 libLLVM-3.4svn.so 0x00000fff917f26f4
> llvm::PassManager::run(llvm::Module&) + 4273352276
> 17 clang 0x00000000103ae874
> 18 clang 0x00000000103af7f8
> clang::EmitBackendOutput(clang::DiagnosticsEngine&,
> clang::CodeGenOptions const&, clang::TargetOptions const&,
> clang::LangOptions const&, llvm::Module*, clang::BackendAction,
> llvm::raw_ostream*) + 4272665128
> 19 clang 0x00000000103ab4a4
> 20 clang 0x000000001059f230 clang::ParseAST(clang::Sema&, bool, bool)
> + 4274649152
> 21 clang 0x00000000101e4b64 clang::ASTFrontendAction::ExecuteAction()
> + 4270836484
> 22 clang 0x00000000103a9b00 clang::CodeGenAction::ExecuteAction() +
> 4272641808
> 23 clang 0x00000000101e4fb4 clang::FrontendAction::Execute() +
> 4270837524
> 24 clang 0x00000000101be154
> clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) +
> 4270679924
> 25 clang 0x000000001019f894
> clang::ExecuteCompilerInvocation(clang::CompilerInstance*) +
> 4270560804
> 26 clang 0x00000000101959d8 cc1_main(char const**, char const**, char
> const*, void*) + 4270520648
> 27 clang 0x000000001019d540 main + 4270551792
> 28 libc.so.6 0x00000080c374bcf8
> 29 libc.so.6 0x00000080c374bef0 __libc_start_main + 4293374496
> Stack dump:
> 0. Program arguments:
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/clang
> -cc1 -fopenmp -triple powerpc64-bgq-linux -S -disable-free
> -main-file-name update.c -static-define -mrelocation-model static
> -mdisable-fp-elim -ffp-contract=fast -mconstructor-aliases
> -target-cpu a2q -target-linker-version 2.20.51.0.2 -coverage-file
> /tmp/update-4ebfb8.s -resource-dir
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/../lib/clang/3.4
> -D __bgclang__=1 -D __bgclang_version__="r000000-00000000" -D
> HAVE_CONFIG_H -D NDEBUG -I
> /bgsys/local/clang/llvm.r190771/r190771-20130914/sleef/include -I
> /bgsys/local/clang/llvm.r190771/r190771-20130914/omp/include -I
> /bgsys/drivers/V1R2M1/ppc64/comm/include -I
> /bgsys/drivers/V1R2M1/ppc64/comm/lib/gnu -I
> /bgsys/drivers/V1R2M1/ppc64 -I
> /bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I
> /bgsys/drivers/V1R2M1/ppc64/spi/include -I
> /bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/src
> -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/include
> -I
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/include
> -I /homeb/zdv518/zdv518/progs/bgsys-clang/include -I
> /bgsys/drivers/V1R2M1/ppc64/comm/include -internal-isystem
> /usr/local/include -internal-isystem
> /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/../lib/clang/3.4/include
> -internal-externc-isystem /include -internal-externc-isystem
> /usr/include -O1 -Wall -Wno-unused -Wunused-value
> -fno-dwarf-directory-asm -fdebug-compilation-dir
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/build-cmake-release-clang/src/mdlib
> -ferror-limit 19 -fmessage-length 277 -mstackrealign
> -fno-signed-char -fobjc-runtime=gcc
> -fobjc-default-synthesize-properties -fdiagnostics-show-option
> -fcolor-diagnostics -vectorize-slp -isystem
> /bgsys/drivers/V1R2M1/ppc64/gnu-linux/powerpc64-bgq-linux/sys-include
> -mllvm -optimize-regalloc -mllvm -fast-isel=0 -o
> /tmp/update-4ebfb8.s -x c
> /homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/src/mdlib/update.c
> 1. <eof> parser at end of file
> 2. Code generation
> 3. Running pass 'Function Pass Manager' on module
> '/homeb/zdv518/zdv518/git/bluegene-dev-r46-clang-bug-diagnosing/src/mdlib/update.c'.
> 4. Running pass 'Loop Pass Manager' on function '@do_update_md'
> 5. Running pass 'Canonicalize natural loops' on basic block
> '%for.body344'
> clang: error: unable to execute command: Aborted (core dumped)
> clang: error: clang frontend command failed due to signal (use -v to
> see invocation)
> clang version 3.4 (trunk)
> Target: powerpc64-bgq-linux
> Thread model: posix
> clang: note: diagnostic msg: PLEASE submit a bug report to
> http://llvm.org/bugs/ and include the crash backtrace, preprocessed
> source, and associated run script.
> clang: note: diagnostic msg:
> ********************
> 
> PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
> Preprocessed source(s) and associated run script(s) are located at:
> clang: note: diagnostic msg: /tmp/update-69ef65.c
> clang: note: diagnostic msg: /tmp/update-69ef65.sh
> clang: note: diagnostic msg:
> 
> ********************
> 
> Hope that helps :-(
> 
> Mark
> 
> 
> 
> 
> On Sun, Sep 29, 2013 at 9:22 PM, Hal Finkel < hfinkel at anl.gov >
> wrote:
> 
> 
> 
> ----- Original Message -----
> > 
> > Hi,
> > 
> > Thanks, Hank. The good news is I succeeded at dropping in the debug
> > version of that object file to the release build.
> 
> Good. Does it also crash with -O2 or -O1? Also, if autovectorization
> is triggering it, you can try passing -fno-vectorize or
> -fno-slp-vectorize -- if this object file is not performance
> critical, however, then don't worry about it for now.
> 
> -Hal
> 
> 
> 
> > Compile times were
> > extremely pleasing. make mdrun -j 8 took the following numbers of
> > seconds at -O3
> > 
> > XLC debug 99
> > XLC release 253
> > clang debug 46
> > clang release 57
> > 
> > Now, off to look at some more important timing measurements ;-)
> > 
> > Mark
> > 
> > 
> > 
> > 
> > On Sun, Sep 29, 2013 at 8:24 PM, Hal Finkel < hfinkel at anl.gov >
> > wrote:
> > 
> > 
> > 
> > ----- Original Message -----
> > > 
> > > 
> > > Hi all,
> > > 
> > > 
> > > I'm the development manager for GROMACS, which will offer new
> > > SIMD
> > > support for BlueGene/Q in its impending 4.6.4 release. Following
> > > some off-list discussion with Jeff Hammond and Hal Finkel, I was
> > > happy to explore compiling with clang for BlueGene/Q. Today I
> > > tried
> > > the version installed on JUQUEEN (r190771-20130914), as I had
> > > trouble logging into Vesta (support request lodged).
> > > 
> > > 
> > > In debug mode, everything went great. clang even warned about
> > > some
> > > MPI_Alltoall calls that could have had some explicit pointer
> > > casts
> > > to reassure the reader, which I've now patched.
> > > 
> > > 
> > > I even used qpxmath.h for a small handful of SIMD trig functions
> > > we'd
> > > want - that worked perfectly.
> > > 
> > > 
> > > In release mode, there was a fatal error from clang when
> > > compiling
> > > the "plain C" version of the code for which I've now written SIMD
> > > kernels. This kernel is compiled and built into mdrun as a
> > > fallback.
> > > My guess would be that auto-vectorization is choking, but
> > > hopefully
> > > you guys are better judges of that than me! I'm happy to pass
> > > this
> > > upstream to LLVM if that's the correct place for this report. The
> > > .c
> > > and .sh files to reproduce the issue can be found at
> > 
> > Thanks for the bug report! This is an error in the backend
> > (although
> > it certainly could be the autovectorization that is exposing it).
> > I'll fix this soon.
> > 
> > 
> > 
> > > 
> > > 
> > > https://docs.google.com/file/d/0B0H2SbsMc3_qTnVvcTI1OTNFMFE/edit?usp=sharing
> > > https://docs.google.com/file/d/0B0H2SbsMc3_qenZBX05KSEg1TnM/edit?usp=sharing
> > > 
> > > 
> > > The crash trace follows:
> > > 
> > > 
> > > 
> > > clang:
> > > /gpfs/vesta-home/hfinkel/rpmbuild/BUILD/llvm/lib/CodeGen/SelectionDAG/DAGCombiner.cpp:630:
> > > llvm::SDValue<unnamed>::DAGCombiner::CombineTo(llvm::SDNode*,
> > > const
> > > llvm::SDValue*, unsigned int, bool): Assertion `N->getNumValues()
> > > ==
> > > NumTo && "Broken CombineTo call!"' failed.
> > > 0 libLLVM-3.4svn.so 0x00000fff7ec34a9c
> > > llvm::sys::PrintStackTrace(_IO_FILE*) + 4281424836
> > > 1 libLLVM-3.4svn.so 0x00000fff7ec34d00
> > > 2 libLLVM-3.4svn.so 0x00000fff7ec35ba4
> > > 3 0x00000fff7f980418 __kernel_sigtramp_rt64 + 0
> > > 4 libc.so.6 0x00000080c3766ef8 abort + 4293479848
> > > 5 libc.so.6 0x00000080c375b98c
> > > 6 libc.so.6 0x00000080c375baa4 __assert_fail + 4293437492
> > > 7 libLLVM-3.4svn.so 0x00000fff7ea0a94c
> > > 8 libLLVM-3.4svn.so 0x00000fff7ea0adfc
> > > 9 libLLVM-3.4svn.so 0x00000fff7ea2de20
> > > 10 libLLVM-3.4svn.so 0x00000fff7ea43554
> > > 11 libLLVM-3.4svn.so 0x00000fff7ea46ecc
> > > 12 libLLVM-3.4svn.so 0x00000fff7ea49c70
> > > llvm::SelectionDAG::Combine(llvm::CombineLevel,
> > > llvm::AliasAnalysis&, llvm::CodeGenOpt::Level) + 4279456680
> > > 13 libLLVM-3.4svn.so 0x00000fff7eb8fba8
> > > llvm::SelectionDAGISel::CodeGenAndEmitDAG() + 4280770368
> > > 14 libLLVM-3.4svn.so 0x00000fff7eb909f8
> > > llvm::SelectionDAGISel::SelectBasicBlock(llvm::ilist_iterator<llvm::Instruction
> > > const>, llvm::ilist_iterator<llvm::Instruction const>, bool&) +
> > > 4280774016
> > > 15 libLLVM-3.4svn.so 0x00000fff7eb92dec
> > > llvm::SelectionDAGISel::SelectAllBasicBlocks(llvm::Function
> > > const&)
> > > + 4280783188
> > > 16 libLLVM-3.4svn.so 0x00000fff7eb93fbc
> > > llvm::SelectionDAGISel::runOnMachineFunction(llvm::MachineFunction&)
> > > + 4280787732
> > > 17 libLLVM-3.4svn.so 0x00000fff7e84d9c8
> > > 18 libLLVM-3.4svn.so 0x00000fff7e1e26cc
> > > llvm::MachineFunctionPass::runOnFunction(llvm::Function&) +
> > > 4270867196
> > > 19 libLLVM-3.4svn.so 0x00000fff7e4529b8
> > > llvm::FPPassManager::runOnFunction(llvm::Function&) + 4273352968
> > > 20 libLLVM-3.4svn.so 0x00000fff7e452afc
> > > llvm::FPPassManager::runOnModule(llvm::Module&) + 4273353276
> > > 21 libLLVM-3.4svn.so 0x00000fff7e4522bc
> > > llvm::MPPassManager::runOnModule(llvm::Module&) + 4273351228
> > > 22 libLLVM-3.4svn.so 0x00000fff7e4525e4
> > > llvm::PassManagerImpl::run(llvm::Module&) + 4273352020
> > > 23 libLLVM-3.4svn.so 0x00000fff7e4526f4
> > > llvm::PassManager::run(llvm::Module&) + 4273352276
> > > 24 clang 0x00000000103ae874
> > > 25 clang 0x00000000103af7f8
> > > clang::EmitBackendOutput(clang::DiagnosticsEngine&,
> > > clang::CodeGenOptions const&, clang::TargetOptions const&,
> > > clang::LangOptions const&, llvm::Module*, clang::BackendAction,
> > > llvm::raw_ostream*) + 4272665128
> > > 
> > > 26 clang 0x00000000103ab4a4
> > > 27 clang 0x000000001059f230 clang::ParseAST(clang::Sema&, bool,
> > > bool)
> > > + 4274649152
> > > 28 clang 0x00000000101e4b64
> > > clang::ASTFrontendAction::ExecuteAction()
> > > + 4270836484
> > > 29 clang 0x00000000103a9b00 clang::CodeGenAction::ExecuteAction()
> > > +
> > > 4272641808
> > > 30 clang 0x00000000101e4fb4 clang::FrontendAction::Execute() +
> > > 4270837524
> > > 31 clang 0x00000000101be154
> > > clang::CompilerInstance::ExecuteAction(clang::FrontendAction&) +
> > > 4270679924
> > > 32 clang 0x000000001019f894
> > > clang::ExecuteCompilerInvocation(clang::CompilerInstance*) +
> > > 4270560804
> > > 33 clang 0x00000000101959d8 cc1_main(char const**, char const**,
> > > char
> > > const*, void*) + 4270520648
> > > 34 clang 0x000000001019d540 main + 4270551792
> > > 35 libc.so.6 0x00000080c374bcf8
> > > 36 libc.so.6 0x00000080c374bef0 __libc_start_main + 4293374496
> > > Stack dump:
> > > 0. Program arguments:
> > > /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/clang
> > > -cc1 -fopenmp -triple powerpc64-bgq-linux -S -disable-free
> > > -main-file-name nbnxn_kernel_ref.c -static-define
> > > -mrelocation-model
> > > static -mdisable-fp-elim -ffp-contract=fast -mconstructor-aliases
> > > -target-cpu a2q -target-linker-version 2.20.51.0.2 -coverage-file
> > > /tmp/nbnxn_kernel_ref-bb4750.s -resource-dir
> > > /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/../lib/clang/3.4
> > > -D __bgclang__=1 -D __bgclang_version__="r000000-00000000" -D
> > > HAVE_CONFIG_H -D md_EXPORTS -D NDEBUG -I
> > > /bgsys/local/clang/llvm.r190771/r190771-20130914/sleef/include -I
> > > /bgsys/local/clang/llvm.r190771/r190771-20130914/omp/include -I
> > > /bgsys/drivers/V1R2M1/ppc64/comm/include -I
> > > /bgsys/drivers/V1R2M1/ppc64/comm/lib/gnu -I
> > > /bgsys/drivers/V1R2M1/ppc64 -I
> > > /bgsys/drivers/V1R2M1/ppc64/comm/sys/include -I
> > > /bgsys/drivers/V1R2M1/ppc64/spi/include -I
> > > /bgsys/drivers/V1R2M1/ppc64/spi/include/kernel/cnk -I
> > > /homeb/zdv518/zdv518/git/bluegene-dev-r46/build-cmake-clang/src
> > > -I
> > > /homeb/zdv518/zdv518/git/bluegene-dev-r46/build-cmake-clang/include
> > > -I /homeb/zdv518/zdv518/git/bluegene-dev-r46/include -I
> > > /homeb/zdv518/zdv518/progs/bgsys-clang/include -I
> > > /bgsys/drivers/V1R2M1/ppc64/comm/include -internal-isystem
> > > /usr/local/include -internal-isystem
> > > /usr/local/bg_soft/clang/llvm.r190771/r190771-20130914/bin/../lib/clang/3.4/include
> > > -internal-externc-isystem /include -internal-externc-isystem
> > > /usr/include -O3 -Wall -Wno-unused -Wunused-value
> > > -fno-dwarf-directory-asm -fdebug-compilation-dir
> > > /homeb/zdv518/zdv518/git/bluegene-dev-r46/build-cmake-clang/src/mdlib
> > > -ferror-limit 19 -fmessage-length 108 -mstackrealign
> > > -fno-signed-char -fobjc-runtime=gcc
> > > -fobjc-default-synthesize-properties -fdiagnostics-show-option
> > > -fcolor-diagnostics -vectorize-loops -vectorize-slp -isystem
> > > /bgsys/drivers/V1R2M1/ppc64/gnu-linux/powerpc64-bgq-linux/sys-include
> > > -mllvm -optimize-regalloc -mllvm -fast-isel=0 -o
> > > /tmp/nbnxn_kernel_ref-bb4750.s -x c
> > > /homeb/zdv518/zdv518/git/bluegene-dev-r46/src/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
> > > 1. <eof> parser at end of file
> > > 2. Code generation
> > > 3. Running pass 'Function Pass Manager' on module
> > > '/homeb/zdv518/zdv518/git/bluegene-dev-r46/src/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c'.
> > > 4. Running pass 'PowerPC DAG->DAG Pattern Instruction Selection'
> > > on
> > > function '@nbnxn_kernel_ref_rf_noener'
> > > 
> > > clang: error: unable to execute command: Aborted (core dumped)
> > > clang: error: clang frontend command failed due to signal (use -v
> > > to
> > > see invocation)
> > > clang version 3.4 (trunk)
> > > Target: powerpc64-bgq-linux
> > > Thread model: posix
> > > clang: note: diagnostic msg: PLEASE submit a bug report to
> > > http://llvm.org/bugs/ and include the crash backtrace,
> > > preprocessed
> > > source, and associated run script.
> > > clang: note: diagnostic msg:
> > > ********************
> > > 
> > > 
> > > PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
> > > Preprocessed source(s) and associated run script(s) are located
> > > at:
> > > clang: note: diagnostic msg: /tmp/nbnxn_kernel_ref-96ac7c.c
> > > clang: note: diagnostic msg: /tmp/nbnxn_kernel_ref-96ac7c.sh
> > > clang: note: diagnostic msg:
> > > 
> > > 
> > > ********************
> > > 
> > > 
> > > I tried to check that the .sh file would reproduce the above, but
> > > it
> > > failed with
> > > 
> > > 
> > > 
> > > In file included from <built-in>:167:
> > > <command line>:6:10: fatal error: 'qpxintrin.h' file not found
> > > #include "qpxintrin.h"
> > 
> > Ah, I keep forgetting to add this to my TODO list to fix. Thanks
> > for
> > reminding me :)
> > 
> > 
> > > 
> > > Hope that is useful - do let me know if I can be of further help!
> > 
> > Quite useful.
> > 
> > -Hal
> > 
> > > 
> > > 
> > > Cheers,
> > > 
> > > 
> > > Mark
> > > _______________________________________________
> > > llvm-bgq-discuss mailing list
> > > llvm-bgq-discuss at lists.alcf.anl.gov
> > > https://lists.alcf.anl.gov/mailman/listinfo/llvm-bgq-discuss
> > > 
> > 
> > --
> > Hal Finkel
> > Assistant Computational Scientist
> > Leadership Computing Facility
> > Argonne National Laboratory
> > 
> > 
> > _______________________________________________
> > llvm-bgq-discuss mailing list
> > llvm-bgq-discuss at lists.alcf.anl.gov
> > https://lists.alcf.anl.gov/mailman/listinfo/llvm-bgq-discuss
> > 
> 
> --
> Hal Finkel
> Assistant Computational Scientist
> Leadership Computing Facility
> Argonne National Laboratory
> 
> 

-- 
Hal Finkel
Assistant Computational Scientist
Leadership Computing Facility
Argonne National Laboratory

-- 
Hal Finkel
Assistant Computational Scientist
Leadership Computing Facility
Argonne National Laboratory