Not yet - waiting for the cards to arrive - hopefully should have something in the next couple of weeks.
I expect it to sit about half way between the Pro 4500 and the Pro 6000 numbers and is indeed likely to be the sweet spot. - For AMBER MD and things like CryoEM (Relion, Cryospark etc).
All the best
Ross
> On Sep 26, 2025, at 12:35, Emme Burgin via AMBER <amber.ambermd.org> wrote:
>
> 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
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!Mih3wA!DnqgsnJcoBQqZr71sqiCWyB7mQRjZREef8qwwcVTRXwEFk0hb0kSZFf993_jHjrO6CJ-JlxpkfA$
> or, via email, send a message with subject or body 'help' to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> 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://urldefense.com/v3/__https://www.dropbox.com/scl/fi/fl9izl2kngja2use841ma/Amber24_Benchmark_Suite.tar.gz?rlkey=d5ft7pd1zebm5b6hf5vrt8gsh__;!!Mih3wA!DnqgsnJcoBQqZr71sqiCWyB7mQRjZREef8qwwcVTRXwEFk0hb0kSZFf993_jHjrO6CJ-4jQoE7Y$
>
> 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
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> This message came from outside your organization.
>
> ZjQcmQRYFpfptBannerEnd
>
> 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
>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!Mih3wA!DnqgsnJcoBQqZr71sqiCWyB7mQRjZREef8qwwcVTRXwEFk0hb0kSZFf993_jHjrO6CJ-JlxpkfA$
>>
> -------------- 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
> -------------- next part --------------
> A non-text attachment was scrubbed...
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>
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>
> Subject: Digest Footer
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> End of AMBER Digest, Vol 4808, Issue 1
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Received on Fri Sep 26 2025 - 13:00:03 PDT
