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<p>Hi,</p>
<p>What is the state of this preliminary work? Is it somehow
useable?</p>
<p>I am wondering if I should look into including openblas in
bootstrap or make use of the conda branch.</p>
<p>How much work and how easy would it be to include openblas in
bootsrap? Basically I just need to download the archive, run make
and make install into base.</p>
<p>Regards,<br>
Pascal<br>
</p>
<br>
<div class="moz-cite-prefix">On 20/06/18 18:54, Billy Poon wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAHmYUca6tyCYYDynu8mq_HDBrqteOOyBV-uQVRGSExvic65QEg@mail.gmail.com">
<div dir="ltr">Hi Luc,
<div><br>
</div>
<div>Also, we are exploring the use of conda for installing the
dependencies instead of compiling from scratch. There is some
preliminary work in <a
href="https://github.com/cctbx/conda_build" target="_blank"
moz-do-not-send="true">https://github.com/cctbx/conda_build</a>
for dependencies and the "conda_compiler" branch in
cctbx_project for building. The "cctbx_dependencies" conda
package already installs mkl and it would be easy to install
openblas.</div>
<div><br>
</div>
<div>This should be ready in a few months once some other
details (e.g. building releases, filling in missing
dependencies) are worked out.</div>
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<div dir="ltr" class="m_-6523680582168579687gmail_signature">
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<div>--</div>
<div><span
style="font-size:12.8000001907349px">Billy
K. Poon</span><br>
</div>
</div>
<div>Research Scientist, Molecular
Biophysics and Integrated
Bioimaging</div>
<div>Lawrence Berkeley National
Laboratory</div>
<div>1 Cyclotron Road, M/S 33R0345</div>
<div>Berkeley, CA 94720</div>
<div>Tel: (510) 486-5709</div>
<div>Fax: (510) 486-5909</div>
<div>Web: <a
href="https://phenix-online.org"
target="_blank"
moz-do-not-send="true">https://phenix-online.org</a></div>
</div>
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<br>
<div class="gmail_quote">
<div dir="ltr">On Wed, Jun 20, 2018 at 9:48 AM Nigel Moriarty
<<a href="mailto:nwmoriarty@lbl.gov" target="_blank"
moz-do-not-send="true">nwmoriarty@lbl.gov</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Luc</div>
<div><br>
</div>
<div>I like the idea. I may be able to convince a new
collaborator to drop FORTRAN in favour of the cctbx.<br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
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<div
class="m_-6523680582168579687m_6509176147846570712gmail_signature"
data-smartmail="gmail_signature">
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<div dir="ltr">Cheers
<div><br>
</div>
<div>Nigel
<div><br>
</div>
<div>---</div>
<div>Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and
Integrated Bioimaging</div>
<div>Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email :
<a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a
href="http://CCI.LBL.gov" target="_blank"
moz-do-not-send="true">CCI.LBL.gov</a></div>
</div>
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<br>
<div class="gmail_quote">On Wed, Jun 20, 2018 at 5:13 AM,
Luc Bourhis <span dir="ltr"><<a
href="mailto:luc_j_bourhis@mac.com" target="_blank"
moz-do-not-send="true">luc_j_bourhis@mac.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi,
<div><br>
</div>
<div>years ago, I had wrote on this discussion list
about a project of mine to dramatically accelerate
scitbx.lstbx by using optimised BLAS libraries. That
work had been dormant on a branch but now we are
planning to move forward with the help of Pascal
Parlois who will do the actual coding in the coming
months. In order for this new code to be exercised
by nightly tests, we, the smtbx people, need to
write code so that that optimised BLAS library is
installed during bootstrap. Right now, as a stopgap,
I used conda to install either OpenBLAS and MKL but
that won’t do with the cctbx philosophy.</div>
<div><br>
</div>
<div>There are basically two choices: either OpenBLAS
or MKL. When I started this project, I chose
OpenBLAS because MKL was not freely redistributable,
and I had got the green light to install it as
needed. However now MKL has become completely free,
thus becoming a possible choice. MKL is more
performant on Intel but OpenBLAS is better on AMD
(OpenBLAS actually runs on pretty much any processor
out there but we don’t care in the context of
cctbx): c.f. <a
href="https://discourse.julialang.org/t/openblas-is-faster-than-intel-mkl-on-amd-hardware-ryzen/8033"
target="_blank" moz-do-not-send="true">Julia
people conclusions</a> Now I realise that most of
you may not care one way or another!?! But we won’t
move forward before we got the green light…</div>
<div><br>
</div>
<div>Note that I am taking about installing a BLAS
usable from C++ here, not getting a BLAS-accelerated
numpy. The latter could be an alternative though.
But that would require to modify the bootstrap code
to compile a MKL- or OpenBLAS-enabled numpy anyway.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Luc J Bourhis</div>
<div><br>
</div>
</div>
<br>
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