Dear All,
I hope you are well.
I am writing to request assistance with installing the GPU‑accelerated
molecular dynamics engine pmemd.cuda from Amber26.
I have a valid academic license for Amber26. I installed AmberTools26
successfully via conda (dacase::ambertools-dac=26) and have also tried
compiling pmemd.cuda from the official source tarballs
(ambertools26.tar.bz2 and pmemd26.tar.bz2) using the recommended CMake
build system.
However, I have encountered a persistent GLIBC version mismatch at the
final linking stage. The errors are of the form:
undefined reference to `pthread_rwlock_wrlock.GLIBC_2.34'
undefined reference to `__cxa_thread_atexit_impl.GLIBC_2.18'
undefined reference to `pow.GLIBC_2.29'
undefined reference to `exp.GLIBC_2.29'
I am using a conda‑provided GCC 15 toolchain, which expects newer GLIBC
symbols (≥2.29), while the system GLIBC appears to be older (likely 2.17 or
2.28). The system libstdc++ library is incompatible with the conda
compiler, causing the linker to fail.
I have tried the following workarounds without success:
Adding -pthread and -no-pie linker flags
Setting -rpath to the conda lib directory
Building both the single‑precision (SPFP) and double‑precision (DPFP)
versions
Disabling all non‑essential tools (e.g., sander, cpptraj, xray, gpu_utils)
At this point, the compilation is blocked by system‑level library
compatibility that I cannot resolve on my own.
I kindly request your assistance
Thank you and Best regards.
*Dr: Ahmed Elrashedy*
Pharmaceutical Chemistry (Ph.D)
Computational Biology and Drug Design Research Lab
Pharmaceutical and Drug Industries Research Institute.
National Research Center
El Behouth St., Dokki, Cairo
Egypt
P.O.Box 12662
Mobile: 002-01029767703
E-mail : aa.elrashedy.nrc.sci.eg
*Website* : https://www.nrc.sci.eg/
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Received on Mon Jul 06 2026 - 02:00:02 PDT
