Not exactly; more that a version is being specified, and I have it, but an OS from some other time period may not, and the same might be true in the reverse. Sometimes in a pinch, you can get away with a symlink or something (you’ll see that some libraries in system directories already do this), but in most cases that’s not advisable/probably would have been done by the distro if it were a reasonable option.
> On Dec 16, 2020, at 5:29 PM, Kenneth Huang <kennethneltharion.gmail.com> wrote:
>
> Hi Ryan,
>
> Aha, I see what you mean- it's subbing in the old libraries with the new
> ones?.I guess whatever effect it has no one could say until you test it,
> but guess can't be helped given the time lapse between now and back then.
> But I'll keep it in mind if I ever do find a copy anywhere.
>
> Best,
>
> Kenneth
>
> On Wed, Dec 16, 2020 at 4:02 PM Ryan Novosielski <novosirj.rutgers.edu>
> wrote:
>
>> It depends on the software package. I’ve definitely tried to run stuff
>> after an upgrade or on a different system or that was installed by package
>> that expected a slightly different operating system and been told “such and
>> such lib.so.5 missing,” and seeing either lib.so.4 or lib.so.6 present on
>> the system. This is sort of moot as you don’t have a copy right now, but
>> you’ll see in this output here some places where you might have a problem,
>> depending on the build:
>>
>> # ldd -v
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20/bin/sander
>> linux-vdso.so.1 => (0x00007fffcd781000)
>> libemil.so =>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libemil.so
>> (0x00007fcc6ef09000)
>> libsff_fortran.so =>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libsff_fortran.so
>> (0x00007fcc6eced000)
>> libnetcdff.so.6 =>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libnetcdff.so.6
>> (0x00007fcc6ea79000)
>> libnetcdf.so.13 =>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libnetcdf.so.13
>> (0x00007fcc6e7a5000)
>> libdl.so.2 => /lib64/libdl.so.2 (0x00007fcc6e5a1000)
>> libfftw3.so.3 => /lib64/libfftw3.so.3 (0x00007fcc6e21c000)
>> libarpack.so =>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libarpack.so
>> (0x00007fcc6dfff000)
>> liblapack.so =>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/liblapack.so
>> (0x00007fcc6dd00000)
>> libblas.so =>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libblas.so
>> (0x00007fcc6dad1000)
>> libm.so.6 => /lib64/libm.so.6 (0x00007fcc6d7cf000)
>> libz.so.1 => /lib64/libz.so.1 (0x00007fcc6d5b9000)
>> libstdc++.so.6 => /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>> (0x00007fcc6d236000)
>> libgfortran.so.4 =>
>> /opt/sw/packages/gcc/7.4/lib64/libgfortran.so.4 (0x00007fcc6ce64000)
>> libgcc_s.so.1 => /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> (0x00007fcc6cc4d000)
>> libquadmath.so.0 =>
>> /opt/sw/packages/gcc/7.4/lib64/libquadmath.so.0 (0x00007fcc6ca0e000)
>> libc.so.6 => /lib64/libc.so.6 (0x00007fcc6c640000)
>> /lib64/ld-linux-x86-64.so.2 (0x00007fcc6f133000)
>>
>> Version information:
>>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20/bin/sander:
>> libgcc_s.so.1 (GCC_3.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libgcc_s.so.1 (GCC_4.0.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libstdc++.so.6 (GLIBCXX_3.4) =>
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>> libstdc++.so.6 (CXXABI_1.3) =>
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>> libdl.so.2 (GLIBC_2.2.5) => /lib64/libdl.so.2
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>> libgfortran.so.4 (GFORTRAN_7) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgfortran.so.4
>>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libemil.so:
>> libgcc_s.so.1 (GCC_3.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>> libstdc++.so.6 (CXXABI_1.3) =>
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>> libstdc++.so.6 (CXXABI_1.3.8) =>
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>> libstdc++.so.6 (GLIBCXX_3.4.11) =>
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>> libstdc++.so.6 (GLIBCXX_3.4.9) =>
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>> libstdc++.so.6 (GLIBCXX_3.4) =>
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>> libstdc++.so.6 (GLIBCXX_3.4.21) =>
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6
>>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libsff_fortran.so:
>> libgfortran.so.4 (GFORTRAN_7) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgfortran.so.4
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libnetcdff.so.6:
>> libgfortran.so.4 (GFORTRAN_7) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgfortran.so.4
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libnetcdf.so.13:
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>> libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> /lib64/libdl.so.2:
>> ld-linux-x86-64.so.2 (GLIBC_PRIVATE) =>
>> /lib64/ld-linux-x86-64.so.2
>> libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> /lib64/libfftw3.so.3:
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>> libc.so.6 (GLIBC_2.3.4) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.4) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libarpack.so:
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>> libgfortran.so.4 (GFORTRAN_7) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgfortran.so.4
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/liblapack.so:
>> libgcc_s.so.1 (GCC_4.0.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libgfortran.so.4 (GFORTRAN_7) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgfortran.so.4
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>>
>> /opt/sw/packages/gcc-7_4/mvapich2-2_3/cuda-10_0/amber/20//lib/libblas.so:
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> libgfortran.so.4 (GFORTRAN_7) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgfortran.so.4
>> /lib64/libm.so.6:
>> ld-linux-x86-64.so.2 (GLIBC_PRIVATE) =>
>> /lib64/ld-linux-x86-64.so.2
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
>> /lib64/libz.so.1:
>> libc.so.6 (GLIBC_2.3.4) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.4) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> /opt/sw/packages/gcc/7.4/lib64/libstdc++.so.6:
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>> ld-linux-x86-64.so.2 (GLIBC_2.3) =>
>> /lib64/ld-linux-x86-64.so.2
>> libgcc_s.so.1 (GCC_4.2.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libgcc_s.so.1 (GCC_3.3) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libgcc_s.so.1 (GCC_3.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.16) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.17) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.3.2) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> /opt/sw/packages/gcc/7.4/lib64/libgfortran.so.4:
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>> libgcc_s.so.1 (GCC_4.2.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libgcc_s.so.1 (GCC_3.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libgcc_s.so.1 (GCC_3.3) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libgcc_s.so.1 (GCC_4.3.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1
>> libquadmath.so.0 (QUADMATH_1.0) =>
>> /opt/sw/packages/gcc/7.4/lib64/libquadmath.so.0
>> libc.so.6 (GLIBC_2.6) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.7) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.17) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
>> /opt/sw/packages/gcc/7.4/lib64/libgcc_s.so.1:
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> /opt/sw/packages/gcc/7.4/lib64/libquadmath.so.0:
>> libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.10) => /lib64/libc.so.6
>> libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
>> libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
>> /lib64/libc.so.6:
>> ld-linux-x86-64.so.2 (GLIBC_2.3) =>
>> /lib64/ld-linux-x86-64.so.2
>> ld-linux-x86-64.so.2 (GLIBC_PRIVATE) =>
>> /lib64/ld-linux-x86-64.so.2
>>
>> --
>> #BlackLivesMatter
>> ____
>> || \\UTGERS, |---------------------------*O*---------------------------
>> ||_// the State | Ryan Novosielski - novosirj.rutgers.edu
>> || \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
>> || \\ of NJ | Office of Advanced Research Computing - MSB C630, Newark
>> `'
>>
>>> On Dec 16, 2020, at 3:49 PM, Kenneth Huang <kennethneltharion.gmail.com>
>> wrote:
>>>
>>> Hi Ryan,
>>>
>>> Would the current libraries contribute that much of a difference? I don't
>>> expect them to be identical to say 3rd or 4th decimal place, but even
>>> considering rounding and precision, shouldn't it be similar? Disclosure-
>>> I've never tried testing Amber compilations across different libraries.
>>>
>>> My very rough grasp of its timeline makes me think 1990-1996? The Amber7
>>> manual is dated to 2002, so I'd guess it'd have been built on Debaian 1.0
>>> or maybe even earlier?
>>>
>>> Best,
>>>
>>> Kenneth
>>>
>>> On Wed, Dec 16, 2020 at 12:35 PM Ryan Novosielski <novosirj.rutgers.edu>
>>> wrote:
>>>
>>>> -----BEGIN PGP SIGNED MESSAGE-----
>>>> Hash: SHA1
>>>>
>>>> I think that's probably unlikely. Even in cases where cases where a
>>>> piece of software compiles fine on either, if it builds against a
>>>> specific version of a library (whatever.so.5), it's probably not going
>>>> to work out on the newer one. Not sure when Amber 4 was from,
>>>> though/what OS would have been current. I don't think I've come across
>>>> older than 11 myself. Would that then be from 2004? So I guess RHEL
>>>> 2-3/Debian 3.0 timeframe?
>>>>
>>>> On 12/16/20 12:54 AM, Kenneth Huang wrote:
>>>>> Hi Bill,
>>>>>
>>>>> Yeah, that was my next try, since I naively thought sander
>>>>> shouldn't have changed too much that present day libraries may
>>>>> work? Though I've had little luck in finding any one with the
>>>>> source code or much documentation from that far back- I knew it was
>>>>> a very, very long stretch, given how far back I'm digging.
>>>>>
>>>>> Best,
>>>>>
>>>>> Kenneth
>>>>>
>>>>> On Tue, Dec 15, 2020 at 11:20 PM Bill Ross <ross.cgl.ucsf.edu>
>>>>> wrote:
>>>>>
>>>>>> I'd find a copy of the source and compile it. Probably
>>>>>> sander/cpu wouldn't be a lot of work to do. A binary from then
>>>>>> might expect old libs to be in place.
>>>>>>
>>>>>> Bill
>>>>>>
>>>>>> On 12/15/20 2:37 PM, Kenneth Huang wrote:
>>>>>>> Hi all,
>>>>>>>
>>>>>>> A very strange question- does anyone happen to have, or know
>>>>>>> anyone who
>>>>>> has
>>>>>>> the old binaries for Amber 4 gathering dust on a hard disk?
>>>>>>>
>>>>>>> I'm having something of a debate about whether the minimization
>>>>>>> procedure in what was shipped in Amber 4 (assuming done in
>>>>>>> sander?) would be comperable to minimization in contemporary
>>>>>>> Amber (specifically sander in Amber 16,18, 20) builds given the
>>>>>>> same setup, parameters, etc. Given
>>>>>> sander
>>>>>>> is one of the older parts of Amber, my thought is that it
>>>>>>> shouldn't have changed much?
>>>>>>>
>>>>>>> Barring the unlikely chance anyone has still code that old
>>>>>>> around still, would there be any good way to test to see if the
>>>>>>> minization changed in a signficant way? My first thought was to
>>>>>>> find a minimized test structure
>>>>>> in
>>>>>>> the source code that might date back from that time, but I
>>>>>>> haven't had
>>>>>> much
>>>>>>> luck in sifting through the test folder so far.
>>>>
>>>> - --
>>>> #BlackLivesMatter
>>>> ____
>>>> || \\UTGERS, |----------------------*O*------------------------
>>>> ||_// the State | Ryan Novosielski - novosirj.rutgers.edu
>>>> || \\ University | Sr. Technologist - 973/972.0922 ~*~ RBHS Campus
>>>> || \\ of NJ | Office of Advanced Res. Comp. - MSB C630, Newark
>>>> `'
>>>> -----BEGIN PGP SIGNATURE-----
>>>>
>>>> iF0EARECAB0WIQST3OUUqPn4dxGCSm6Zv6Bp0RyxvgUCX9pFSAAKCRCZv6Bp0Ryx
>>>> vjZYAKCV6iHVkW4/N5LcKYCraChPzL1VlwCeP7wYHTlkj2bLcRfgKfY8dMD1Nxk=
>>>> =xEl6
>>>> -----END PGP SIGNATURE-----
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> --
>>> Ask yourselves, all of you, what power would hell have if those
>> imprisoned
>>> here could not dream of heaven?
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
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Received on Wed Dec 16 2020 - 15:00:02 PST
