Does anyone have benchmarks (even if not for the full suite) for the RTX PRO 5000 Blackwell? In previous architecture generations the 5000 card has been an excellent balance between cost and performance.
From: amber-request.ambermd.org <amber-request.ambermd.org>
Date: Friday, September 26, 2025 at 3:05 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: AMBER Digest, Vol 4808, Issue 1
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AMBER Mailing List Digest
Today's Topics:
1. Re: Updated Amber 24 benchmarks (Ross Walker)
2. miniconda error with Amber24 (Jiang, Wei)
3. Re: miniconda error with Amber24 (David A Case)
4. Re: miniconda error with Amber24 (Jiang, Wei)
5. Re: miniconda error with Amber24 (Skanda Sastry)
----------------------------------------------------------------------
Message: 1
Date: Thu, 25 Sep 2025 12:26:02 -0700
From: Ross Walker <ross.rosswalker.co.uk>
To: "David A. Case" <dacase1.gmail.com>
Cc: AMBER Mailing List <amber.ambermd.org>, Oscar Conchillo-Sol?
<Oscar.Conchillo.uab.cat>
Subject: Re: [AMBER] Updated Amber 24 benchmarks
Message-ID: <08E5B141-B1FD-4D4F-80D7-5DC97EEE9935.rosswalker.co.uk>
Content-Type: text/plain; charset=utf-8
Hi Oscar,
You can use this link: wget https://www.dropbox.com/scl/fi/fl9izl2kngja2use841ma/Amber24_Benchmark_Suite.tar.gz?rlkey=d5ft7pd1zebm5b6hf5vrt8gsh
That's the set I used to run the benchmarks that appear on Exxact's website.
All the best
Ross
> On Sep 25, 2025, at 11:45, David A Case <dacase1.gmail.com> wrote:
>
> On Tue, Sep 23, 2025, Oscar Conchillo-Sol? via AMBER wrote:
>
>> By any chance anybody knows if the files to reproduce exactly the same runs as Exxact people did are somewhere?. I would like to run them in my computers so I can truly compare.
>
> The link was accidentally removed from the Amber web site. You can now to
> to ambermd.org, and navigate to GPU Support -> Benchmarks to access the
> link.
>
> ...dac
>
> p.s. cc-ing to Ross Walker, in case any updates are needed.
>
------------------------------
Message: 2
Date: Thu, 25 Sep 2025 19:46:51 +0000
From: "Jiang, Wei" <wjiang.alcf.anl.gov>
To: 'AMBER Mailing List' <amber.ambermd.org>
Subject: [AMBER] miniconda error with Amber24
Message-ID:
<PH0PR09MB11822A8AF4034AAC2F5375616F31FA.PH0PR09MB11822.namprd09.prod.outlook.com>
Content-Type: text/plain; charset="koi8-r"
Hi, I am trying to re-install Amber24 on an Nvidia A100 cluster. Last December run_cmake worked fine and I got Amber24 installed successfully. But now with the identical code I see the following error when running run_cmake. It looks like miniconda is installing something incompatible with the existing software environment. This did not happen before. Can anybody advise how to avoid it?
LibMambaUnsatisfiableError: Encountered problems while solving:
- package cython-0.29-py27he6710b0_0 requires python >=2.7,<2.8.0a0, but none of the providers can be installed
Could not solve for environment specs
The following packages are incompatible
?? cython =0.29 * is installable with the potential options
? ?? cython [0.29|0.29.10|...|0.29.8] would require
? ? ?? python >=2.7,<2.8.0a0 *, which can be installed;
? ?? cython [0.29|0.29.10|...|0.29.8] would require
? ? ?? python >=3.6,<3.7.0a0 *, which can be installed;
? ?? cython [0.29|0.29.10|...|0.29.8] would require
? ? ?? python >=3.7,<3.8.0a0 *, which can be installed;
? ?? cython [0.29.13|0.29.14|...|0.29.37] would require
? ? ?? python >=3.8,<3.9.0a0 *, which can be installed;
? ?? cython [0.29.21|0.29.22|...|0.29.37] would require
? ? ?? python >=3.9,<3.10.0a0 *, which can be installed;
? ?? cython [0.29.25|0.29.28|...|0.29.37] would require
? ? ?? python >=3.10,<3.11.0a0 *, which can be installed;
? ?? cython [0.29.32|0.29.33|0.29.35|0.29.36|0.29.37] would require
? ? ?? python >=3.11,<3.12.0a0 *, which can be installed;
? ?? cython [0.29.36|0.29.37] would require
? ?? python >=3.12,<3.13.0a0 *, which can be installed;
?? pin on python 3.13.* =* * is not installable because it requires
?? python =3.13 *, which conflicts with any installable versions previously reported.
Pins seem to be involved in the conflict. Currently pinned specs:
- python=3.13
Thanks & Regards
Wei Jiang, PhD, Computational Science Division
Argonne National Laboratory
9700S, Cass Ave, Lemont, IL60439
630-252-8688<callto:630-252-8688> (office)
630-252-7121<callto:630-252-7121> (fax)
------------------------------
Message: 3
Date: Thu, 25 Sep 2025 14:20:22 -0600
From: David A Case <dacase1.gmail.com>
To: "Jiang, Wei" <wjiang.alcf.anl.gov>, AMBER Mailing List
<amber.ambermd.org>
Subject: Re: [AMBER] miniconda error with Amber24
Message-ID: <20250925202022.wnn3dtkkhxr36ezz.pop-os.localdomain>
Content-Type: text/plain; charset=us-ascii; format=flowed
On Thu, Sep 25, 2025, Jiang, Wei via AMBER wrote:
>Hi, I am trying to re-install Amber24 on an Nvidia A100 cluster. Last
>December run_cmake worked fine and I got Amber24 installed
>successfully. But now with the identical code I see the following error
>when running run_cmake. It looks like miniconda is installing something
>incompatible with the existing software environment. This did not happen
>before. Can anybody advise how to avoid it?
Thank you for the report.
It would be helpful to know exactly what commands you used, and what
OS and compiler environment you are using.
It looks like you are trying to install "Amber24" from a year or so ago.
The current versions are AmberTools25 and a re-packaged "Amber24". You
might try downloading the latest versions to see if that would help. Note
that the updated Amber24 (which extracts into the directory tree headed by
"pmemd24_src") has no need for python or miniconda, and should not
encounter the errors you report.
It's hard to tell if AmberTools25 (which does download miniconda) would
encounter these problems; no one else has reported this problem, which is why
we would like to know more about your OS environment.
That said, it looks like the whole thing is related to cython-0.29 somehow.
I don't understand what is going on, since the AmberTools25 code that
is distributed has already been cythonized, and should have no reason to
look for a particular version of cython. It is certainly possible that
there is an error in the miniconda install options that is just now causing
problems.
Others on the list, better versed in miniconda and python/cython, may be
able to offer better insights.
...hope this helps....dac
------------------------------
Message: 4
Date: Thu, 25 Sep 2025 22:51:06 +0000
From: "Jiang, Wei" <wjiang.alcf.anl.gov>
To: David A Case <dacase1.gmail.com>, AMBER Mailing List
<amber.ambermd.org>
Subject: Re: [AMBER] miniconda error with Amber24
Message-ID:
<PH0PR09MB11822B12639E586D72BC5F279F31FA.PH0PR09MB11822.namprd09.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Thank you so much! I downloaded Amber25tools and the repackaged Amber24 source code, and they compile well. Apparently, the problem is the out-of-dated source files., which might have affected the way conda installs updated Amber.
Best regards
Wei
________________________________
From: David A Case <dacase1.gmail.com>
Sent: Thursday, September 25, 2025 3:20 PM
To: Jiang, Wei <wjiang.alcf.anl.gov>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] miniconda error with Amber24
On Thu, Sep 25, 2025, Jiang, Wei via AMBER wrote: >Hi, I am trying to re-install Amber24 on an Nvidia A100 cluster. Last >December run_cmake worked fine and I got Amber24 installed >successfully. But now with the identical code I see
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This Message Is From an External Sender
This message came from outside your organization.
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On Thu, Sep 25, 2025, Jiang, Wei via AMBER wrote:
>Hi, I am trying to re-install Amber24 on an Nvidia A100 cluster. Last
>December run_cmake worked fine and I got Amber24 installed
>successfully. But now with the identical code I see the following error
>when running run_cmake. It looks like miniconda is installing something
>incompatible with the existing software environment. This did not happen
>before. Can anybody advise how to avoid it?
Thank you for the report.
It would be helpful to know exactly what commands you used, and what
OS and compiler environment you are using.
It looks like you are trying to install "Amber24" from a year or so ago.
The current versions are AmberTools25 and a re-packaged "Amber24". You
might try downloading the latest versions to see if that would help. Note
that the updated Amber24 (which extracts into the directory tree headed by
"pmemd24_src") has no need for python or miniconda, and should not
encounter the errors you report.
It's hard to tell if AmberTools25 (which does download miniconda) would
encounter these problems; no one else has reported this problem, which is why
we would like to know more about your OS environment.
That said, it looks like the whole thing is related to cython-0.29 somehow.
I don't understand what is going on, since the AmberTools25 code that
is distributed has already been cythonized, and should have no reason to
look for a particular version of cython. It is certainly possible that
there is an error in the miniconda install options that is just now causing
problems.
Others on the list, better versed in miniconda and python/cython, may be
able to offer better insights.
...hope this helps....dac
------------------------------
Message: 5
Date: Thu, 25 Sep 2025 16:44:08 -0700
From: Skanda Sastry <skandasastry.gmail.com>
To: "Jiang, Wei" <wjiang.alcf.anl.gov>, AMBER Mailing List
<amber.ambermd.org>
Subject: Re: [AMBER] miniconda error with Amber24
Message-ID:
<CACTQ5mVTtxn881o9TrjN7z-Gzk1ZfvifbJ=if_oiYLiDTRvzzQ.mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello Prof. Jiang,
I don't know if this will fix your specific issue but I wanted to send over
a conda YML file that I use to set my Amber conda environment. In addition
to this I also have attached the set of modules I load using lmod when
compiling Amber. If you load these Lmod modules and load this conda
environment you should be able to routinely compile Amber successfully.
This has been my solution to the myriad dependency issues that Amber can
produce during compilation.
Regards,
Skanda
On Thu, Sep 25, 2025 at 12:47?PM Jiang, Wei via AMBER <amber.ambermd.org>
wrote:
> Hi, I am trying to re-install Amber24 on an Nvidia A100 cluster. Last
> December run_cmake worked fine and I got Amber24 installed successfully.
> But now with the identical code I see the following error when running
> run_cmake. It looks like miniconda is installing something incompatible
> with the existing software environment. This did not happen before. Can
> anybody advise how to avoid it?
>
> LibMambaUnsatisfiableError: Encountered problems while solving:
> - package cython-0.29-py27he6710b0_0 requires python >=2.7,<2.8.0a0, but
> none of the providers can be installed
> Could not solve for environment specs
> The following packages are incompatible
> ?? cython =0.29 * is installable with the potential options
> ? ?? cython [0.29|0.29.10|...|0.29.8] would require
> ? ? ?? python >=2.7,<2.8.0a0 *, which can be installed;
> ? ?? cython [0.29|0.29.10|...|0.29.8] would require
> ? ? ?? python >=3.6,<3.7.0a0 *, which can be installed;
> ? ?? cython [0.29|0.29.10|...|0.29.8] would require
> ? ? ?? python >=3.7,<3.8.0a0 *, which can be installed;
> ? ?? cython [0.29.13|0.29.14|...|0.29.37] would require
> ? ? ?? python >=3.8,<3.9.0a0 *, which can be installed;
> ? ?? cython [0.29.21|0.29.22|...|0.29.37] would require
> ? ? ?? python >=3.9,<3.10.0a0 *, which can be installed;
> ? ?? cython [0.29.25|0.29.28|...|0.29.37] would require
> ? ? ?? python >=3.10,<3.11.0a0 *, which can be installed;
> ? ?? cython [0.29.32|0.29.33|0.29.35|0.29.36|0.29.37] would require
> ? ? ?? python >=3.11,<3.12.0a0 *, which can be installed;
> ? ?? cython [0.29.36|0.29.37] would require
> ? ?? python >=3.12,<3.13.0a0 *, which can be installed;
> ?? pin on python 3.13.* =* * is not installable because it requires
> ?? python =3.13 *, which conflicts with any installable versions
> previously reported.
> Pins seem to be involved in the conflict. Currently pinned specs:
> - python=3.13
>
> Thanks & Regards
>
> Wei Jiang, PhD, Computational Science Division
> Argonne National Laboratory
> 9700S, Cass Ave, Lemont, IL60439
> 630-252-8688<callto:630-252-8688> (office)
> 630-252-7121<callto:630-252-7121> (fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
-------------- next part --------------
Currently Loaded Modules:
1) Miniforge3/24.1.2-0 10) ncurses/6.2-GCCcore-9.3.0 19) numactl/2.0.13-GCCcore-9.3.0 28) OpenSSL/1.1 37) arpack-ng/3.7.0-foss-2020a
2) GCCcore/9.3.0 11) util-linux/2.35-GCCcore-9.3.0 20) XZ/5.2.5-GCCcore-9.3.0 29) libarchive/3.6.1-GCCcore-9.3.0 38) gzip/1.10-GCCcore-9.3.0
3) zlib/1.2.11-GCCcore-9.3.0 12) fontconfig/2.13.92-GCCcore-9.3.0 21) libxml2/2.9.10-GCCcore-9.3.0 30) CMake/3.26.3-GCCcore-9.3.0 39) lz4/1.9.2-GCCcore-9.3.0
4) binutils/2.34-GCCcore-9.3.0 13) xorg-macros/1.19.2-GCCcore-9.3.0 22) hwloc/2.2.0-GCCcore-9.3.0 31) OpenBLAS/0.3.9-GCC-9.3.0 40) zstd/1.4.4-GCCcore-9.3.0
5) GCC/9.3.0 14) libpciaccess/0.16-GCCcore-9.3.0 23) libevent/2.1.11-GCCcore-9.3.0 32) gompi/2020a 41) Boost/1.72.0-gompi-2020a
6) bzip2/1.0.8-GCCcore-9.3.0 15) X11/20200222-GCCcore-9.3.0 24) libfabric/1.11.0-GCCcore-9.3.0 33) ScaLAPACK/2.1.0-gompi-2020a 42) UCX/1.14.1-GCCcore-9.3.0
7) expat/2.2.9-GCCcore-9.3.0 16) libreadline/8.0-GCCcore-9.3.0 25) PMIx/3.1.5-GCCcore-9.3.0 34) FFTW/3.3.8-gompi-2020a 43) GDRCopy/2.3.1-GCCcore-9.3.0
8) libpng/1.6.37-GCCcore-9.3.0 17) Perl/5.30.2-GCCcore-9.3.0 26) OpenMPI/4.0.3-GCC-9.3.0 35) foss/2020a 44) NCCL/2.8.3-GCCcore-9.3.0-CUDA-11.0.2
9) freetype/2.10.1-GCCcore-9.3.0 18) CUDAcore/11.0.2 27) cURL/7.69.1-GCCcore-9.3.0 36) Eigen/3.3.7-GCCcore-9.3.0 45) APBS/3.0.0-7738be6-foss-2020a
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Received on Fri Sep 26 2025 - 13:00:02 PDT
