- cctbxbb - phenix-online.org

normalize() is not safe
by Oleg Sobolev 02 May '17

02 May '17

Dear colleagues, I recently discovered that normalize() function of scitbx::vec3<double> is not safe, i.e. this case scitbx::vec3<double> a(0,0,0); a.normalize(); it will produce division by zero and fail. If function contains this being called from python the traceback would be rather vague: <...> Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. The code that generates this error sits in scitbx/vec3.h, lines 143-153 with a comment that this was done intentionally and a pointer to an appropriate function to do safe normalization. This function is not wrapped to be available in python directly. Similar functionality (but coded in a different place) accessible via python by: >>> from scitbx import matrix >>> b = matrix.col([0,0,0]) >>> b.normalize() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/net/anaconda/raid1/olegs/phenix_queue/modules/cctbx_project/scitbx/matrix/__init__.py", line 270, in normalize return self / abs(self) File "/net/anaconda/raid1/olegs/phenix_queue/modules/cctbx_project/scitbx/matrix/__init__.py", line 158, in __truediv__ return rec([e/other for e in self.elems], self.n) ZeroDivisionError: float division by zero Fast grepping shows that normalize() is widely used in xfel, smtbx, rstbx, dxtbx, mmtbx/hydrogens, scitbx/rigid_body, and in some other places. My questions to CCTBX community are: 1. Were you aware of this issue? 2. Should we do something about it: - make the function more safe and slow; - leave it like it is and let everybody know about the issue and let developers deal with it individually; 3. Any other input on the matter? Best regards, Oleg Sobolev.

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Boost Python 1.56
by Luc Bourhis 14 Apr '17

14 Apr '17

Hi, I have improvements to the smtbx on their way to be committed which require Boost version 1.56. This is related to Boost.Threads, whose support I re-activated a few months ago on Nick’s request. I need the function boost::thread::physical_concurrency which returns the number of physical cores on the machine, as opposed to virtual cores when hyperthreading is enabled (which it is by default on any Intel machine). That function is not available in Boost 1.55 which is the version currently used in the nightly tests: it appeared in 1.56. So, would it be possible to move to Boost 1.56? Otherwise, I will need to backport that function. Not too difficult but not thrilling. Best wishes, Luc

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Re: [cctbxbb] [git/cctbx] master: Replacing illegal C++ code with proper dynamic array allocation. (a31eb2bf0)
by Nicholas Sauter 12 Apr '17

12 Apr '17

Rob, Just as a general thing, "new" statements in C++ need to be paired with "delete" statements (delete pk, delete a_sum, and delete akml). Unless this is done there will be a memory leak. Nick Nicholas K. Sauter, Ph. D. Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Tue, Apr 11, 2017 at 3:31 AM, CCTBX Commit via DLS Jenkins < graeme.winter(a)gmail.com> wrote: > Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbx > On branch : master > > ------------------------------ > > > commit a31eb2bf0d5bb129425bb759466f45622c773fd4 > Author: Robert Oeffner <rdo20(a)cam.ac.uk> > Date: Tue Apr 11 11:31:24 2017 +0100 > > Replacing illegal C++ code with proper dynamic array allocation. > > > ------------------------------ > > > a31eb2bf0d5bb129425bb759466f45622c773fd4 > scitbx/lbfgs.h | 6 +++--- > 1 file changed, 3 insertions(+), 3 deletions(-) > > diff --git a/scitbx/lbfgs.h b/scitbx/lbfgs.h > index 41be8e8cc..f0000143d 100755 > --- a/scitbx/lbfgs.h > +++ b/scitbx/lbfgs.h > @@ -917,9 +917,9 @@ namespace lbfgs { > int info = 5; > brackt = false; > FloatType sxnorm = std::sqrt(ddot(SizeType(n), sx, sx)); > - FloatType pk[n]; > - FloatType a_sum[n]; > - FloatType akm1[n]; > + FloatType* pk = new FloatType[n]; > + FloatType* a_sum = new FloatType[n]; > + FloatType* akm1 = new FloatType[n]; > for (SizeType i=0; i < n; i++) { > pk[i] = sx[i]/sxnorm; > akm1[i] = -gx[i]/sxnorm; >

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libtiff dependency on macOS
by Billy Poon 11 Apr '17

11 Apr '17

Hi everyone, I just updated install_base_packages.py to build libtiff generally instead of just for Linux. So if you update your sources and get build errors relating to TIFF, please rebuild your base directory. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [cctbxbb] bug fix in cctbx_project/scitbx/lbfgs.h
by R.D. Oeffner 11 Apr '17

11 Apr '17

There is now a fatal warning in libtbx/SConscript if gcc encounters variable length arrays as this is not portable code and we've had broken builds on more than one occasion due to this recently. Rob On 11/04/2017 12:01, Pavel Afonine wrote: > Hi Rob, > > thanks for the fix. This is was Min's code (remember her from the past workshop?). I simply applied her patch without looking into it too much, and made sure all t96 pass. > > Again, thanks for fixing it. > > Pavel > > On 4/11/17 03:48, R.D. Oeffner wrote: > >> Hi Pavel, I have made a change to that file as it didn't compile on Windows. In fact I can't understand how it would compile with other compilers before as the syntax to me seemed illegal given that n is not known at compile time. I'm not sure how a dynamically created FloatType should be destroyed as I couldn't find any examples of that being done throughout this file. Rob

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bootstrap.py on windows
by Horst Puschmann 07 Apr '17

07 Apr '17

Hello I am trying to install the cctbx on a Windows 7 64 bit machine using the following bootstrap.py file: https://raw.githubusercontent.com/cctbx/cctbx_project/master /libtbx/auto_build/bootstrap.py The script will fail, unless I comment out lines 1101 and 1102: #if self.isPlatformWindows(): #tarurl, arxname, dirpath = MODULES.get_module(module)(). get_tarauthenticated(auth=self.get_auth()) If it tries to execute the commented lines, the error will be "KeyError: 'cciuser' in line 590" After commenting this out, it will fail in line 271, with "AttributeError: 'module' object has no attribute '_create_unverified_context'" I can get round that with disabling line 247: if sys.platform == "win32": (i.e. change this to if sys.platform == "xxx":) After that, things start downloading. All appears well until the same thing happens again in another bootstrap.py file in \modules\cctbx_project\ libtbx\auto_build\bootstrap.py If I disable *that*, it goes further but fails finally with ===== Running in build: run configure.py Traceback (most recent call last): File "bootstrap.py", line 2113, in <module> run() File "bootstrap.py", line 2108, in run enable_shared=options.enable_shared, File "bootstrap.py", line 1036, in run i.run() File "bootstrap.py", line 189, in run raise RuntimeError("Could not run %s: File not found" % executable) RuntimeError: Could not run base\bin\python: File not found I guess the automatic tests haven't picked this up, because no authentication is needed, maybe? Greetings Horst

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Fw: cctbx developer guidelines
by R. D. Oeffner 06 Apr '17

06 Apr '17

Hi Pavel and others, Attached is the original word document you sent out if that's useful for anyone. Rob -----Original Message----- From: Pavel Afonine Sent: Saturday, July 11, 2015 7:12 PM To: Paul Adams ; developers(a)phenix-online.org Subject: Re: cctbx developer guidelines Hi Paul, looks great! Attached is slightly edited copy. Pavel On 7/10/15 11:14, Paul Adams wrote: > Hi Everyone, > > we have developed a cctbx developer guidance document (much of which > also applies to Phenix development). I’m attaching it for your review and > comments. If you have any suggestions let me know. The goal is to > distribute this to all developers who are contributing to the cctbx and to > put it somewhere prominent on the web. > > Cheers, > Paul >

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bootstrap.py not overwriting modified sources
by R.D. Oeffner 01 Apr '17

01 Apr '17

Hi all, It appears that when bootstrap.py is invoked to update sources then unsurprisingly it doesn't overwrite existing sources if these are more recent, as in someone has modified them and not committed the changes. Occasionally this leads to broken builds. To prevent this from happening would it not be a good idea to change bootstrap.py to default to overwrite any uncommitted changes unless some flag is set on the command line? Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 mobile: +44(0)7712 887162

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Berkeley Server Downtime (3/23 - 3/24)
by Billy Poon 24 Mar '17

24 Mar '17

Dear all, On Thursday, March 23, our servers will be shut down starting at 5:00 pm Pacific for some emergency electrical work near our building. We expect that the servers will be available the next day (3/24) by 1:00 pm Pacific. There is a possibility that the outage will last longer. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience and the short notice. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [cctbxbb] cctbxbb Digest, Vol 96, Issue 3
by Allan Lyckegaard 22 Mar '17

22 Mar '17

Hi Billy, Thanks, it works! It now compiles and when adding it to the path, “source build/setpaths.sh”, it can be imported in python. A few questions, though: - is it necessary to create a new conda environment to make it work? My first try where I got the error was in an existing environment. - can I update any packages in my new environment without breaking cctbx? I would i.e. be wonderful to have access to ipython Cheers, Allan ******************************************************** Allan Lyckegaard, PhD, Scientist Xnovo Technology ApS Galoche Alle 15 4600 Køge CVR: 3489 4221 Mail: alyckegaard(a)xnovotech.com <mailto:[email protected]> Mobile: +45 5373 8581 ******************************************************* The information in this email, including any attachments, is confidential and intended only for the recipient(s) listed. Any use of this email for any other purpose is prohibited. If you have received this email in error, please notify me immediately by reply email, delete this email, and do not disclose its contents to anyone. > On 21 Mar 2017, at 20.00, cctbxbb-request(a)phenix-online.org wrote: > > Send cctbxbb mailing list submissions to > cctbxbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/cctbxbb > or, via email, send a message with subject or body 'help' to > cctbxbb-request(a)phenix-online.org > > You can reach the person managing the list at > cctbxbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of cctbxbb digest..." > > > Today's Topics: > > 1. Re: Build error, bootstrap.py (Billy Poon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 20 Mar 2017 12:38:31 -0700 > From: Billy Poon <bkpoon(a)lbl.gov> > To: cctbx mailing list <cctbxbb(a)phenix-online.org> > Subject: Re: [cctbxbb] Build error, bootstrap.py > Message-ID: > <CAHmYUcY2oJp=D9w_de=S++fn4D9rzanB+zFtqU8ME9OgWmSu-Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Allan, > > Your command should have installed the hdf5 dependency among the other > dependencies. The hdf5 dependency is required because there are functions > for reading image data. Was there an error in compiling HDF5? There should > be a log file in <cctbx installation directory>/base_tmp named > HDF5_install_log. > > Are you using a recent version of bootstrap.py? I just tested this on macOS > 10.12.3 with conda 4.3.11 and the command-line tools for Xcode 8.2.1. The > steps I followed (in a clean directory with just bootstrap.py) are, > > 1) conda create -n test python=2 > 2) source activate test > 3) python bootstrap.py --with-python=`which python` --builder=cctbx > --nproc=8 > 4) cd build; make > > The `which python` command in step 3 just returns the path for the python > in the "test" environment. Step 4 is just to make sure everything is > compiled. > > Let us know if you it still does not work. Thanks! > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > On Fri, Mar 17, 2017 at 7:27 AM, Allan Lyckegaard <alyckegaard(a)xnovotech.com >> wrote: > >> Hi all, >> >> I am trying to install cctbx on my Mac (Sierra) using bootstrap.py with my >> Anaconda python. >> >> When executing 'python bootstrap.py --with-python=/Users/myuser/ >> miniconda2/envs/python2/bin/python --builder=cctbx? I get the following >> error: >> >> /usr/bin/c++ -o dxtbx/format/boost_python/nexus_ext.o -c >> -DBOOST_HAS_INT128=1 -DBOOST_ALL_NO_LIB -DBOOST_PYTHON_MAX_BASES=2 -Wmost >> -Wno-unknown-pragmas -Wno-logical-op-parentheses -Wno-unused-local-typedefs >> -I/Users/myuser/Development/cctbx/modules/boost -fPIC >> -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 >> -ffast-math -I/Users/myuser/miniconda2/envs/python2/include >> -I/Users/myuser/Development/cctbx/base/include >> -I/Users/myuser/Development/cctbx/build/include >> -I/Users/myuser/Development/cctbx/modules/cctbx_project >> -I/Users/myuser/miniconda2/envs/python2/include/python2.7 >> /Users/myuser/Development/cctbx/modules/cctbx_project/ >> dxtbx/format/boost_python/nexus_ext.cc >> warning: unknown warning option '-Wno-unused-local-typedefs' >> [-Wunknown-warning-option] >> 1 warning generated. >> /usr/bin/c++ -o lib/dxtbx_format_nexus_ext.so -w -bundle -undefined >> dynamic_lookup dxtbx/format/boost_python/nexus_ext.o >> -L/Users/myuser/Development/cctbx/base/lib -lm -lhdf5 >> ld: library not found for -lhdf5 >> clang: error: linker command failed with exit code 1 (use -v to see >> invocation) >> scons: *** [lib/dxtbx_format_nexus_ext.so] Error 1 >> scons: building terminated because of errors. >> usr+sys time: 8.69 seconds >> wall clock time: 21.70 seconds >> Process failed with return code 2 >> >> Any suggestions to how I solve this? I have not seen anywhere in the >> documentation that an hdf5 installation is a prerequisite. >> >> Cheers, >> /Allan >> >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >

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