Hi,
I wanted to report an issue that I encountered when compiling Amber24 (and resolution). I am not sure if others encountered this, but I hope my report might be useful to those who do.
Setup: I am running my compilation with CUDA 10.2, gcc 8.5, OpenMPI 4.1.5, python 3.10, and cmake 3.25.2 on a Red Hat Enterprise Linux release 8.8 (Ootpa) system.
Error: Making and compilation proceeds without issue until reaching 95%. At this point, the following error is encountered:
“nvcc fatal : redefinition of argument 'std'
CMake Error at pmemd_cuda_SPFP_generated_kXray.cu.o.RELEASE.cmake:219 (message):
Error generating
/<path>/amber24_src/build/src/pmemd/src/cuda/CMakeFiles/pmemd_cuda_SPFP.dir//./pmemd_cuda_SPFP_generated_kXray.cu.o”
Looking more closely at the verbose output, I noticed that “--std c++11” was appended to the command that generates the error. “-std=c++14” is already specified in the command, causing the re-definition to terminate the compilation.
The fix is to comment out line 254 in PMEMDCompilerFlags.cmake:
#list(APPEND PMEMD_NVCC_FLAGS --std c++11)
This allows the compilation to complete without error.
Best,
Mayukh Chakrabarti (he/him)
COMPUTATIONAL SCIENTIST
From: David A Case via AMBER <amber.ambermd.org>
Date: Wednesday, May 1, 2024 at 12:20 PM
To: amber.ambermd.org <amber.ambermd.org>, amber-developers.ambermd.org <amber-developers.ambermd.org>
Subject: [EXTERNAL] [AMBER] Release of Amber24 and AmberTools24
On behalf of the Amber development team, I am pleased to announce the
release of Amber24 and AmberTools24. Thanks to all who contributed to this.
Details and downloading instructions are here:
https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fambermd.org%2F&data=05%7C02%7Cmayukh.chakrabarti%40nih.gov%7Cf4679ca3c5614357941108dc69fa9e4e%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638501772317750459%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=LZlRhVvnFeSxNe76Vpuvm%2FA4G84xWxk13J4TVmocRSo%3D&reserved=0<
https://ambermd.org/>
Some notes:
* There is no license fee for non-commercial use.
* We are still working on the lists of new features, but there are lots
of these.
* The conda package for AmberTools24 is not yet ready. We'll update the
web page and post an email when it becomes available
* See the Installation tab on the menu at the left for instructions for
various operating systems.
* Please use the Amber mailing list reflector to report problems. Given
the wide variety of hardware and software environments out there, we
won't be surprised, but will try our best to address issues that arise.
...dave case
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Received on Mon May 06 2024 - 10:00:01 PDT
