Compile gromacs with nvhpc 23.5 on arm64

juntang · June 12, 2023, 2:53am

I am trying to build gromacs 22.4 with nvhpc 23.5 on arm64 and run into the following error (related to int64_t). Is there any walk around this?

cd /shared/tools/gromacs-2022.4/build_mpi-nvhpc/src/gromacs && /shared/nvidia/hpc_sdk/Linux_aarch64/23.5/comm_libs/mpi/bin/mpicxx -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DMUPARSER_STATIC -DTMPI_EXPORTS -DTMPI_USE_VISIBILITY -DUSE_STD_INTTYPES_H -I/shared/tools/gromacs-2022.4/src/include -I/shared/tools/gromacs-2022.4/build_mpi-nvhpc/src/include -I/shared/tools/gromacs-2022.4/src -I/shared/tools/gromacs-2022.4/api/legacy/include -I/shared/tools/gromacs-2022.4/build_mpi-nvhpc/api/legacy/include -I/shared/tools/gromacs-2022.4/src/gromacs/analysisdata/include -I/shared/tools/gromacs-2022.4/src/gromacs/utility/include -I/shared/tools/gromacs-2022.4/src/gromacs/applied_forces/include -I/shared/tools/gromacs-2022.4/src/gromacs/commandline/include -I/shared/tools/gromacs-2022.4/src/gromacs/compat/include -I/shared/tools/gromacs-2022.4/src/gromacs/coordinateio/include -I/shared/tools/gromacs-2022.4/src/gromacs/correlationfunctions/include -I/shared/tools/gromacs-2022.4/src/gromacs/domdec/include -I/shared/tools/gromacs-2022.4/src/gromacs/essentialdynamics/include -I/shared/tools/gromacs-2022.4/src/gromacs/ewald/include -I/shared/tools/gromacs-2022.4/src/gromacs/fft/include -I/shared/tools/gromacs-2022.4/src/gromacs/fileio/include -I/shared/tools/gromacs-2022.4/src/gromacs/gmxana/include -I/shared/tools/gromacs-2022.4/src/gromacs/gmxlib/include -I/shared/tools/gromacs-2022.4/src/gromacs/gmxpreprocess/include -I/shared/tools/gromacs-2022.4/src/gromacs/gpu_utils/include -I/shared/tools/gromacs-2022.4/src/gromacs/hardware/include -I/shared/tools/gromacs-2022.4/src/gromacs/imd/include -I/shared/tools/gromacs-2022.4/src/gromacs/linearalgebra/include -I/shared/tools/gromacs-2022.4/src/gromacs/listed_forces/include -I/shared/tools/gromacs-2022.4/src/gromacs/math/include -I/shared/tools/gromacs-2022.4/src/gromacs/mdlib/include -I/shared/tools/gromacs-2022.4/src/gromacs/mdrun/include -I/shared/tools/gromacs-2022.4/src/gromacs/mdrunutility/include -I/shared/tools/gromacs-2022.4/src/gromacs/mdspan/include -I/shared/tools/gromacs-2022.4/src/gromacs/mdtypes/include -I/shared/tools/gromacs-2022.4/src/gromacs/mimic/include -I/shared/tools/gromacs-2022.4/src/gromacs/modularsimulator/include -I/shared/tools/gromacs-2022.4/src/gromacs/nbnxm/include -I/shared/tools/gromacs-2022.4/src/gromacs/onlinehelp/include -I/shared/tools/gromacs-2022.4/src/gromacs/options/include -I/shared/tools/gromacs-2022.4/src/gromacs/pbcutil/include -I/shared/tools/gromacs-2022.4/src/gromacs/pulling/include -I/shared/tools/gromacs-2022.4/src/gromacs/random/include -I/shared/tools/gromacs-2022.4/src/gromacs/restraint/include -I/shared/tools/gromacs-2022.4/src/gromacs/selection/include -I/shared/tools/gromacs-2022.4/src/gromacs/simd/include -I/shared/tools/gromacs-2022.4/src/gromacs/statistics/include -I/shared/tools/gromacs-2022.4/src/gromacs/swap/include -I/shared/tools/gromacs-2022.4/src/gromacs/tables/include -I/shared/tools/gromacs-2022.4/src/gromacs/taskassignment/include -I/shared/tools/gromacs-2022.4/src/gromacs/timing/include -I/shared/tools/gromacs-2022.4/src/gromacs/tools/include -I/shared/tools/gromacs-2022.4/src/gromacs/topology/include -I/shared/tools/gromacs-2022.4/src/gromacs/trajectory/include -I/shared/tools/gromacs-2022.4/src/gromacs/trajectoryanalysis/include -isystem /shared/tools/gromacs-2022.4/src/external/thread_mpi/include -isystem /shared/tools/gromacs-2022.4/src/external -isystem /shared/fftw-3.3.9/include -isystem /shared/tools/gromacs-2022.4/src/external/tng_io/include -isystem /shared/tools/gromacs-2022.4/build_mpi-nvhpc/tng/include -isystem /shared/tools/gromacs-2022.4/src/external/lmfit -isystem /shared/tools/gromacs-2022.4/src/external/muparser/include -std=c++17 -tp=neoverse-v1 -g -fast -O3 -DNDEBUG --c++17 -msve-vector-bits=256 -mp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -MF CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o.d -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp

error messages:

"/shared/tools/gromacs-2022.4/api/legacy/include/gromacs/math/functions.h", line 118: error: expected an identifier
  unsigned int log2I(std::int64_t x);
                          ^

"/shared/tools/gromacs-2022.4/api/legacy/include/gromacs/math/functions.h", line 118: error: declaration is incompatible with "unsigned int gmx::log2I(int32_t)" (declared at line 107)
  unsigned int log2I(std::int64_t x);
               ^

"/shared/tools/gromacs-2022.4/api/legacy/include/gromacs/math/functions.h", line 118: error: expected a ")"
  unsigned int log2I(std::int64_t x);
                          ^

"/shared/tools/gromacs-2022.4/api/legacy/include/gromacs/math/functions.h", line 129: error: declaration is incompatible with "unsigned int gmx::log2I" (declared at line 118)
  unsigned int log2I(std::uint32_t x);
               ^

"/shared/tools/gromacs-2022.4/api/legacy/include/gromacs/math/functions.h", line 140: error: declaration is incompatible with previous "gmx::log2I" (declared at line 118)
  unsigned int log2I(std::uint64_t x);
               ^

"/shared/tools/gromacs-2022.4/api/legacy/include/gromacs/math/functions.h", line 149: error: expected an identifier
  std::int64_t greatestCommonDivisor(std::int64_t p, std::int64_t q);
       ^

"/shared/tools/gromacs-2022.4/api/legacy/include/gromacs/math/functions.h", line 149: error: expected a ";"
  std::int64_t greatestCommonDivisor(std::int64_t p, std::int64_t q);
       ^

"/shared/tools/gromacs-2022.4/src/gromacs/trajectory/trajectoryframe.h", line 123: error: expected an identifier
      std::int64_t step() const;
           ^

"/shared/tools/gromacs-2022.4/src/gromacs/trajectory/trajectoryframe.h", line 123: error: this declaration has no storage class or type specifier
      std::int64_t step() const;
      ^

"/shared/tools/gromacs-2022.4/src/gromacs/trajectory/trajectoryframe.h", line 123: error: expected a ";"
      std::int64_t step() const;
           ^

"/shared/tools/gromacs-2022.4/src/gromacs/utility/mdmodulesnotifiers.h", line 110: error: expected an identifier
      std::int64_t energyCalculationIntervalInSteps() const
           ^

"/shared/tools/gromacs-2022.4/src/gromacs/utility/mdmodulesnotifiers.h", line 110: error: this declaration has no storage class or type specifier
      std::int64_t energyCalculationIntervalInSteps() const
      ^

"/shared/tools/gromacs-2022.4/src/gromacs/utility/mdmodulesnotifiers.h", line 110: error: expected a ";"
      std::int64_t energyCalculationIntervalInSteps() const
           ^

"/shared/tools/gromacs-2022.4/src/gromacs/utility/mdmodulesnotifiers.h", line 121: warning: parsing restarts here after previous syntax error [end_of_flush]
      const std::int64_t energyCalculationIntervalInSteps_;
                                                          ^

Remark: individual warnings can be suppressed with "--diag_suppress <warning-name>"

"/shared/tools/gromacs-2022.4/src/gromacs/utility/mdmodulesnotifiers.h", line 106: error: "energyCalculationIntervalInSteps_" is not a nonstatic data member or base class of class "gmx::EnergyCalculationFrequencyErrors"
          energyCalculationIntervalInSteps_(energyCalculationIntervalInSteps)
          ^

"/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp", line 114: error: expected an identifier
  template void readKvtCheckpointValue(compat::not_null<std::int64_t*> value,
                                                             ^

"/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp", line 114: error: invalid combination of type specifiers
  template void readKvtCheckpointValue(compat::not_null<std::int64_t*> value,
                                                        ^

"/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp", line 132: error: expected an identifier
  template void writeKvtCheckpointValue(const std::int64_t&       value,
                                                   ^

"/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp", line 132: error: explicit type is missing ("int" assumed)
  template void writeKvtCheckpointValue(const std::int64_t&       value,
                                              ^

"/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp", line 132: error: expected a ")"
  template void writeKvtCheckpointValue(const std::int64_t&       value,
                                                   ^

"/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp", line 135: warning: parsing restarts here after previous syntax error [end_of_flush]
                                        KeyValueTreeObjectBuilder kvtBuilder);
                                                                            ^

"/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp", line 132: error: no instance of function template "gmx::writeKvtCheckpointValue" matches the specified type
  template void writeKvtCheckpointValue(const std::int64_t&       value,
                ^

"/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp", line 1203: error: argument of type "int64_t *" is incompatible with parameter of type "long long *"
          do_cpt_step_err(xd, "step", &contents->step, list);
                                      ^

21 errors detected in the compilation of "/shared/tools/gromacs-2022.4/src/gromacs/fileio/checkpoint.cpp".

Regards,

juntang · June 12, 2023, 2:56am

mpicc --version

nvc 23.5-0 linuxarm64 target on aarch64 Linux -tp neoverse-v1
NVIDIA Compilers and Tools
Copyright (c) 2022, NVIDIA CORPORATION & AFFILIATES. All rights reserved.

MatColgrove · June 12, 2023, 8:50pm

Hi juntang,

The “cstdint” header file, which is where these symbols would be defined, would be coming from your system headers.

What g++ do you have installed? Is it an older version which doesn’t support C++17?

-Mat

juntang · June 13, 2023, 1:55am

Mat,

gcc --version
gcc (Ubuntu 11.1.0-1ubuntu1~20.04) 11.1.0
Copyright (C) 2021 Free Software Foundation, Inc

I believe it supports c++17 because I can compile Gromacs with GCC-11.

MatColgrove · June 13, 2023, 4:27pm

I grabbed the Gromacs package and was able to reproduce the error.

Looks to be an issue with the header file “src/gromacs/fileio/xdrf.h” where they define “int64_t” to be a “long long”:

#ifdef __PGI /*Portland group compiler*/
#    define int64_t long long
#endif

For compatibility, we still define “__PGI” and hence this gets included which in turn causes your errors.

I’m not very familiar with gromacs myself, so don’t have a recommended solution, but you might try commenting out this line to see if you get further.

juntang · June 14, 2023, 4:47am

Mat,

This fixes the compiling problem for me. BTW, do you know what’s the recommended blas/lapack library for nvhpc?

MatColgrove · June 14, 2023, 6:30pm

It’s what ever you like but we do ship prepackaged versions which you can use.

system · June 28, 2023, 6:31pm

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Compile gromacs with nvhpc 23.5 on arm64

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