Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build

From: Ross Walker <>
Date: Wed, 24 Oct 2012 12:52:03 -0700

>It is not a problem of gmail's spam filter, it is the best I
>have seen. Even if messages are marked as spam they are
>accessible from Spam folder and go away only after certain
>amount of time. About the real issue at the end.

Agreed but in my experience it gets way too many false positives and if
one is access mail remotely via another client the messages in junk are
not delivered as part of a POP3 connection for example hence they can go
undetected for a long time.

>>The problem is two fold. Firstly gmail can greylist things so message
>> delivery for gmail accounts can often be substantially delayed and
>> gmail is I believe hiding your own copy of the message from you since it
>> is trying to be too smart for it's own good and detecting the same
>> already in your sent items.
>First time I hear that gmail might greylisting mails, never
>happened to me in 5 years. Any noticable delay might be only
>because using email client which checks for mail periodically,
>so they show up in the program only after next check or Google
>is having unconfined server problems (doesn't happen often).

post log
Oct 24 11:30:34 2012 (3322) post to amber from,
size=6179, message-id=<>, success

smtp log
Oct 24 11:30:34 2012 (3322) <> smtp
to amber for 1372 recips, completed in 0.257 seconds

exim main log
2012-10-24 11:30:33 1TR5ir-0000JB-Oj <= [] P=esmtps X=TLSv1:RC4-SHA:128 S
=6108 T="Re: [AMBER] [PATCH 4/8]
sqm: Fix OpenMP build"
2012-10-24 11:30:39 1TR5is-0000JG-NU
[2607:f8b0:400e:c03::1b] Network is unreachable
2012-10-24 11:30:39 1TR5is-0000JG-NU
[2607:f8b0:400e:c03::1b] Network is unreachable

2012-10-24 11:30:48 1TR5is-0000JG-Rj SMTP error from remote mail server
after RCPT TO:<..>: host
[]: 451-4.3.0 Multiple destination domains per transaction is
unsupported. Please\n451 4.3.0 try again. o4si22306281paw.25

2012-10-24 11:30:56 1TR5is-0000JG-Rj SMTP error from remote mail server
after RCPT TO:<..>: host gmail []: 451-4.3.0 Multiple destination
domains per transaction is unsupported. Please\n451 4.3.0 try
 again. f9si22268238paz.203

2012-10-24 11:32:51 1TR5is-0000JG-Rj == .. R=dnslookup
T=remote_smtp defer (-53): retry time not reached for any host


Looks a lot like grey listing to me. Perhaps semantically it is different
but either way it leads to a delay in delivery of mail to some gmail

>> Simple solution is to use a non-gmail account which would actually be
>> better for everyone on the list. People should not be using 'anonymous'
>> accounts to post to what is a scientific discussion list. I am tempted
>> enforce a rule that everyone posting either has an account where we can
>> identify who they are OR signs their email with a signature identifying
>> their full name, institution and affiliation.
>No, that would be a wrong way to go. First, institution mail has
>no place for high volume mailing lists. Second, people's names
>and affiliations has nothing to do with scientific discussions.
>Third, we are not talking here as representatives of our

Actually I beg to differ here. Anonymity has no place science and indeed
one has no right to it when expressing scientific opinions which is the
main basis of this mailing list. To promote discussion of science and
scientific problems as they center around molecular dynamics and the use
of the AMBER molecular dynamics research software. If one chooses in a
scientific community to make statements or offer opinions behind the
shroud of anonymity then such opinions should be viewed with extreme
skepticism. I fully believe that if one wants respect and recognition in
science, which indeed is what scientific reputation is based on then they
should be prepared to stand by any statements they make right or wrong.
This has been the basis of scientific discussion for hundreds of years and
one should not casually dismiss that on the basis that it is now
substantially easier to make comments 'pseudo' anonymously than it used to

As for talking as a representative of your institution, I'm really sorry
to inform you but unfortunately what you are posting is a reflection of
your institutional affiliation. As a graduate student, postdoc or faculty
at a university your voices and opinions as they relate to your work at
said university are a reflection on the university. Indeed, almost all
students and staff have signed a document signing over their work to
ownership by the university. If you are not at a university in some
capacity and/or what you are posting here is in no way related to your
research at the university then you are correct you are not representing
the research group you belong to or your institution. However, if what you
post here relates to your research, or was undertaken during your expected
hours of employment or study then unfortunately you do represent the
institution whether you like it or not.

Relating to my first point about anonymity. Including your details and
institution with your comments also adds significant weight to the value
of such comments since people viewing them will base their opinion on both
your reputation and that of the institution you are at. This is why
research papers have full affiliations listed on them.

>You are already moderating signups for amber-developers which is
>hilarious for publicly readable list. And you have absolutely no
>pointer on website for where to send user contributions for
>AmberTools (Bug tracker? Maintainer mail? Source repository with
>the relevant information around? Give something!). I can tell
>that my little experiment to send these patches was really
>frustrating exactly because of these two reasons.

The moderation of the developers list has nothing to do with posts being
public, it is purely so we have some semi-autonomous control over who
receives emails and announcements sent to that list. It is a pretty simple
matter to subscribe to the list. Simply subscribe, email the list owner
(me) with your affiliation to the AMBER developers or just a very simple
explanation of why you want to receive messages and announcements related
to the development of the code and I'll happily approve the subscription.

As for AmberTools. We have a full bug tracking system that we use
internally and we can add people to that who are happy to use it properly,
appreciating that people's time is very limited. We also have full git
repositories for the code. Given the research nature of the software we
tend to be very wary of accepting user contributions that are sent
directly. It is extremely easy to break such fragile codes and it is also
very easy to write code that gives the wrong answer scientifically.
Community scientific code without control on what gets added can be VERY
dangerous. Thus for almost any scientific code it tends to be better for
contributions to go through the maintainer of that code. The simplest way
to do that is to post to the AMBER mailing list and ask who maintains
various pieces of code. The website says:

"We hope to add new functionality to AmberTools as additional programs
become available. If you have suggestions for what might be added, please
contact us."

Which seems pretty self explanatory to me. The authors of the various
packages are all stated, none of us contribute anonymously, although we
may be extremely busy writing grant proposals and reports these days which
means it can take a few weeks to get replies but it shouldn't be difficult
to contact one of us and then if we are not the right person we'll refer
you to the right person.

In your case a post to the AMBER list asking the best way to make
contributions and explaining what you found would certainly have been the
best starting point. Then be patient and people will contact you. I don't
want to discourage people making contributions. Far from it, we value such
things, it is just that these days, what with current funding climates,
people tend to be extremely overworked and so it is critical to be patient
in such matters.

>> A more complex solution would be to check your gmail settings and see if
>> there is a way to prevent this sort of thing happening but I don't know
>> a solution. If you find one please let me know and I can add it to the
>> list subscription instructions.
>The issue seems to be with gmail as you already suggest. The
>thing is that gmail recognizes duplicates using message IDs and
>removes them without providing a configuration option to change
>this behaviour.
>So the solution would be to set mailman to change message ID (if
>possible) or just document that this particular option will not
>work with gmail (or any other account automatically and
>unconditionally removing mails with the same IDs). The messages
>are still saved (as sent) so they are available, but without any
>modification mailman does to bounced mail.

If you know how to do this, or other recommended mailman settings I'd be
grateful to hear suggestions. I took a look through the various settings
and couldn't see anything immediately obvious for how to have the message
sent with a different message id.

>It would also help if the archive would be updated as soon as
>there are new posts.

It takes over 45 minutes right now to process the mail archive and update
the page. Hence why I have it set to do it just once every few days. It
has been on my radar for a long time to improve this, have it update the
page incrementally rather than reprocessing the entire mail spool, but it
simply hasn't managed to float to the top of my todo list. If you know a
simple way to do it please let me know. I know mailman has an archive
system built in but it is not very flexible and I couldn't see an easy way
of importing 13 years of archived messages into it.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Wed Oct 24 2012 - 13:00:03 PDT
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