Thank you all,
Vlad Cojocaru's patch worked just fine. It was indeed an incompatibility between the Glibc and CUDA.
Thank you again,
Frederico Henrique do Carmo Rufino Ferreira
NEQC-Núcleo de Estudos em Química Computacional
Universidade Federal de Juiz de Fora / Instituto de Ciências Exatas - Departamento de Química
________________________________
From: Frederico Henrique Ferreira via AMBER <amber.ambermd.org>
Sent: 04 April 2026 18:36
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Installation issue - xray module
Good afternoon,
I have been trying to install pmemd package on my Ubuntu system, but I consistently get an error when trying to install it. I am using the following cmake options:
cmake $AMBER_PREFIX/pmemd24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/pmemd24 \
-DCOMPILER=GNU \
-DMPI=TRUE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=FALSE -DBUILD_PYTHON=FALSE \
-DBUILD_PERL=FALSE -DBUILD_GUI=FALSE \
-DPMEMD_ONLY=TRUE -DCHECK_UPDATES=FALSE \
2>&1 | tee cmake.log
[ 6%] Building NVCC (Device) object src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_xray_non_bulk.cu.o
/usr/include/x86_64-linux-gnu/bits/mathcalls.h(83): error: exception specification is incompatible with that of previous function "cospi" (declared at line 2601 of /usr/local/cuda/include/crt/ma
th_functions.h)
extern double cospi (double __x) noexcept (true); extern double __cospi (double __x) noexcept (true);
^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h(85): error: exception specification is incompatible with that of previous function "sinpi" (declared at line 2556 of /usr/local/cuda/include/crt/ma
th_functions.h)
extern double sinpi (double __x) noexcept (true); extern double __sinpi (double __x) noexcept (true);
^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h(206): error: exception specification is incompatible with that of previous function "rsqrt" (declared at line 597 of /usr/local/cuda/include/crt/ma
th_functions.h)
extern double rsqrt (double __x) noexcept (true); extern double __rsqrt (double __x) noexcept (true);
^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h(83): error: exception specification is incompatible with that of previous function "cospif" (declared at line 2623 of /usr/local/cuda/include/crt/m
ath_functions.h)
extern float cospif (float __x) noexcept (true); extern float __cospif (float __x) noexcept (true);
^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h(85): error: exception specification is incompatible with that of previous function "sinpif" (declared at line 2579 of /usr/local/cuda/include/crt/m
ath_functions.h)
extern float sinpif (float __x) noexcept (true); extern float __sinpif (float __x) noexcept (true);
^
/usr/include/x86_64-linux-gnu/bits/mathcalls.h(206): error: exception specification is incompatible with that of previous function "rsqrtf" (declared at line 621 of /usr/local/cuda/include/crt/m
ath_functions.h)
extern float rsqrtf (float __x) noexcept (true); extern float __rsqrtf (float __x) noexcept (true);
^
6 errors detected in the compilation of "/home/fred4h/softwares/pmemd24_src/src/pmemd/src/xray/cuda/src/xray/xray_non_bulk.cu".
CMake Error at pmemd_xray_cuda_generated_xray_non_bulk.cu.o.RELEASE.cmake:278 (message):
Error generating file
/home/fred4h/softwares/pmemd24_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_xray_non_bulk.cu.o
make[2]: *** [src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/build.make:4930: src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_xray_non_bulk.cu.o
] Error 1
make[1]: *** [CMakeFiles/Makefile2:1530: src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
I am currently running Kubuntu 25.10 and I have tried installing alongside cudas 12.6, 12.8 and 13.2, but they all returned the same error.
Thank you,
Frederico Henrique do Carmo Rufino Ferreira
NEQC-Núcleo de Estudos em Química Computacional
Universidade Federal de Juiz de Fora / Instituto de Ciências Exatas - Departamento de Química
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Received on Mon Apr 06 2026 - 07:00:03 PDT
