Okay, this seems to be related with an incompatibility between CUDA
(12,4, 12.6, 12.8) and the Glibc 2.41 (which comes on openSUSE
Tumbleweed). The problem seems to be solved with a rather simple patch
(see below).
Modify the function declarations for cospi, sinpi, cospif, and sinpif in
the CUDA installation:
$CUDA_ROOT/targets/x86_64-linux/include/crt/math_functions.h
With this and with python3.11 (pytraj does not build with python3.13)
the updated Amber24 builds correctly on openSUSE Tumbleweed with GCC
13.3.1 and CUDA 12.4.1 (GLIBC 2.41)
Cheers
Vlad
********************** patch **************************
diff '--color=auto' -ur
builds.orig/cuda_nvcc/targets/x86_64-linux/include/crt/math_functions.h
builds/cuda_nvcc/targets/x86_64-linux/include/crt/math_functions.h
---
a/builds.orig/cuda_nvcc/targets/x86_64-linux/include/crt/math_functions.h
2024-08-23 00:25:39.000000000 +0200
+++ b/builds/cuda_nvcc/targets/x86_64-linux/include/crt/math_functions.h
2025-02-17 01:19:44.270292640 +0100
.. -2547,7 +2547,7 @@
*
* \note_accuracy_double
*/
-extern __DEVICE_FUNCTIONS_DECL__ __device_builtin__
double sinpi(double x);
+extern __DEVICE_FUNCTIONS_DECL__ __device_builtin__
double sinpi(double x) noexcept (true);
/**
* \ingroup CUDA_MATH_SINGLE
* \brief Calculate the sine of the input argument
.. -2570,7 +2570,7 @@
*
* \note_accuracy_single
*/
-extern __DEVICE_FUNCTIONS_DECL__ __device_builtin__
float sinpif(float x);
+extern __DEVICE_FUNCTIONS_DECL__ __device_builtin__
float sinpif(float x) noexcept (true);
/**
* \ingroup CUDA_MATH_DOUBLE
* \brief Calculate the cosine of the input argument
.. -2592,7 +2592,7 @@
*
* \note_accuracy_double
*/
-extern __DEVICE_FUNCTIONS_DECL__ __device_builtin__
double cospi(double x);
+extern __DEVICE_FUNCTIONS_DECL__ __device_builtin__
double cospi(double x) noexcept (true);
/**
* \ingroup CUDA_MATH_SINGLE
* \brief Calculate the cosine of the input argument
.. -2614,7 +2614,7 ..
*
* \note_accuracy_single
*/
-extern __DEVICE_FUNCTIONS_DECL__ __device_builtin__
float cospif(float x);
+extern __DEVICE_FUNCTIONS_DECL__ __device_builtin__
float cospif(float x) noexcept (true);
/**
* \ingroup CUDA_MATH_DOUBLE
* \brief Calculate the sine and cosine of the first input argument
On 3/30/25 10:57 AM, Vlad Cojocaru via AMBER wrote:
> Dear David, Dear all,
>
> Thanks a lot for the detailed answer. Yes, sure, I can try to build
> the new PMEMD with gcc 14 and cuda 12.8. Please feel welcome to share
> the code when you feel its ripped (best is to use my current email
> address "vlad.cojocaru.ubbcluj.ro" )
>
> On a different note, you mentioned the incompatibility between GCC 14
> and CUDA 12.4. However, I did manage to install both CUDA 12.4 and
> 12.8 with GCC 14.2.1 with no issues.
>
> Regarding the current installation, I am still struggling, this time
> with cpptraj. Now, I reverted back to gcc 13 with cuda 12.4. However,
> I am running into different issues now (see below). These issues were
> not there when I first installed Amber24 with this compiler and cuda.
> I tried to go into the CPPTRAJ code but did not find any hint
>
> Best wishes
> Vlad
>
>
> [ 15%] Building CXX object
> AmberTools/src/cpptraj/src/CMakeFiles/cpptraj_core.dir/Matrix_3x3.cpp.o
> make[2]: ***
> [AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/build.make:84:
> AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/cpptraj_cuda_routines_generated_kernel_wrappers.cu.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs....
> [ 15%] Building CXX object
> AmberTools/src/cpptraj/src/CMakeFiles/cpptraj_common_obj_cuda.dir/ActionTopWriter.cpp.o
> [ 15%] Building CXX object
> AmberTools/src/cpptraj/src/CMakeFiles/cpptraj_common_obj.dir/Action_Bounds.cpp.o
> /usr/include/bits/mathcalls.h(79): error: exception specification is
> incompatible with that of previous function "cospi" (declared at line
> 5554 of /apps/nvidia/cuda/12.4.1_gnu-13.3.1/include/crt/math_functions.h)
> extern double cospi (double __x) noexcept (true); extern double
> __cospi (double __x) noexcept (true);
> ^
>
> /usr/include/bits/mathcalls.h(81): error: exception specification is
> incompatible with that of previous function "sinpi" (declared at line
> 5442 of /apps/nvidia/cuda/12.4.1_gnu-13.3.1/include/crt/math_functions.h)
> extern double sinpi (double __x) noexcept (true); extern double
> __sinpi (double __x) noexcept (true);
> ^
>
> /usr/include/bits/mathcalls.h(79): error: exception specification is
> incompatible with that of previous function "cospif" (declared at line
> 5606 of /apps/nvidia/cuda/12.4.1_gnu-13.3.1/include/crt/math_functions.h)
> extern float cospif (float __x) noexcept (true); extern float
> __cospif (float __x) noexcept (true);
> ^
>
> /usr/include/bits/mathcalls.h(81): error: exception specification is
> incompatible with that of previous function "sinpif" (declared at line
> 5502 of /apps/nvidia/cuda/12.4.1_gnu-13.3.1/include/crt/math_functions.h)
> extern float sinpif (float __x) noexcept (true); extern float
> __sinpif (float __x) noexcept (true);
> ^
>
> 4 errors detected in the compilation of
> "/apps/amber/24_tools-24_cuda-12.4.1_openmpi-5.0.3_gnu-13.3.1/AmberTools/src/cpptraj/src/cuda_kernels/GistCudaCalc.cu".
> CMake Error at
> cpptraj_cuda_routines_generated_GistCudaCalc.cu.o.RELEASE.cmake:278
> (message):
> Error generating file
> /apps/amber/24_tools-24_cuda-12.4.1_openmpi-5.0.3_gnu-13.3.1/build/AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir//./cpptraj_cuda_routines_generated_GistCudaCalc.cu.o
>
>
>
> make[2]: ***
> [AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/build.make:91:
> AmberTools/src/cpptraj/src/cuda_kernels/CMakeFiles/cpptraj_cuda_routines.dir/cpptraj_cuda_routines_generated_GistCudaCalc.cu.o]
> Error 1
>
> On 3/29/25 11:54 PM, David A Case wrote:
>> On Sat, Mar 29, 2025, Vlad Cojocaru via AMBER wrote:
>>>
>>> I have now updated the OS on our machines (to latest openSUSE
>>> Tumbleweed snapshot) and I am trying to update the AMBER 24
>>> installation as well. I am using gcc 14.2.1, Cuda 12.4.1, openmpi
>>> 5.0.7.
>>
>>> However I get the error below which is related to "Quick". I tried
>>> to disable Quick (with -DDISABLE_TOOL="quick" in run_cmake) but then
>>> I get some dependency issue for sander (missing libquick). I should
>>> say that I have built Amber 24 successfully with gcc 13.2.1 before.
>>
>> Simplest: install gcc 13.2 and use "alternatives" (or create soft-links,
>> depends on your distro) to have version 13.2 temporarily first in
>> your PATH.
>> Parts of Amber are just not ready for gcc14 (as you have found out.)
>>
>> I think(!) the only part of the current Amber that objects to gcc14
>> is the
>> CUDA part of Quick. (Based on developer reports--I've not tried this
>> myself.) But the main "point" of Quick is its GPU capability, and I
>> don't
>> know what is involved in getting gcc14 compatibility. (It sort of looks
>> like a header failure from the error messages, but I'm really just
>> guessing.) We'll try to get the Quick problem resolved, and maybe
>> someone
>> on the list will have better knowledge than I have. But right now, I
>> don't
>> know when that will happen.
>>
>> One thought: coming in the next release: Amber (essentially pmemd)
>> will be
>> fully separated from AmberTools. For people who mainly want pmemd.cuda,
>> this will allow a much simpler build of that, without exposure to any
>> limitations in the much more complex AmberTools code.
>> If you would like to test this, let me know, and I'll point you to the
>> code, which is now in a near-final release stage. (This would also
>> help us
>> get testing on gcc14 as well as on OpenSUSE, which is less commonly-used
>> in the US.) But it's up to you: the straightforward path is to
>> enable an
>> earlier version of the GNU compiler suite; that might prove useful
>> for other
>> software as well.
>>
>> ...thanks for the report....dac
>>
>
--
Dr. Vlad Cojocaru (PD, Habil.)
----------------------------------------------
Guest Scientist / Fmr. Project Group Leader
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
----------------------------------------------
Email: vlad.cojocaru.mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Sun Mar 30 2025 - 04:30:03 PDT
