Re: [cctbxbb] Molprobity / CCTBX incompatibility

That is the correct directory for the general Phenix install. @Christopher Williams Does the script run bootstrap.py from the current directory or does it cd elsewhere. I have noticed that accessing the repos at Duke can be a problem but I just did so the servers are fine. I still think the "running the install script with bootstrap.py in the current directory" could still be the problem. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 19, 2019 at 10:49 AM Charitha Belluru Shetty < [email protected]> wrote:

Hi Nigel,

Can you please let us know which directory? Since the Molprobity directory is not created after running

*. install_via_bootstrap.sh 10*

The steps to install ideally would be as below:

./install_via_bootstrap.sh 4

cd/molprobity

./setup.sh

But in our case “modules” directory got created.

-bash-4.2$ ls -l

total 131

-rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py

-rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc

-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh

drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules

-bash-4.2$ ls -l modules

total 2913

drwxr-xr-x 11 cbs72396 appmgmt 17 Nov 27 2012 annlib

drwxr-sr-x 8 cbs72396 appmgmt 15 Aug 16 13:38 annlib_adaptbx

-rw-r--r-- 1 cbs72396 appmgmt 519563 Aug 16 05:13 annlib.gz

drwxr-sr-x 5 cbs72396 appmgmt 6 Aug 16 13:38 boost

drwxr-sr-x 20 cbs72396 appmgmt 48 Aug 16 13:38 cbflib

drwxr-xr-x 5 cbs72396 appmgmt 6 Oct 30 2013 ccp4io

drwxr-xr-x 5 cbs72396 appmgmt 30 May 19 17:56 ccp4io_adaptbx

-rw-r--r-- 1 cbs72396 appmgmt 208764 Aug 16 05:13 ccp4io_adaptbx.gz

-rw-r--r-- 1 cbs72396 appmgmt 1417443 Aug 16 05:13 ccp4io.gz

drwxr-sr-x 38 cbs72396 appmgmt 45 Aug 16 13:38 cctbx_project

drwxr-sr-x 5 cbs72396 appmgmt 5 Aug 16 13:37 chem_data

drwxrwxr-x 4 cbs72396 appmgmt 15 Sep 18 2017 scons

-rw-r--r-- 1 cbs72396 appmgmt 636186 Aug 16 05:13 scons.gz

drwxr-xr-x 4 cbs72396 appmgmt 11 Aug 19 2009 tntbx

-rw-r--r-- 1 cbs72396 appmgmt 38909 Aug 16 05:13 tntbx.gz

Best Regards,

Charitha Shetty

*From:* Nigel Moriarty *Sent:* Monday, August 19, 2019 1:08 PM *To:* Christopher Williams *Cc:* Charitha Belluru Shetty ; Robert Nolte ; [email protected] *Subject:* Re: Molprobity / CCTBX incompatibility

*EXTERNAL*

Sorry guy, I was on holidays and the maintenance was a problem.

Try putting the bootstrap.py in the directory that the command is being run.

Cheers

Nigel

---

Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Fri, Aug 16, 2019 at 7:27 PM Christopher Williams < [email protected]> wrote:

Hmm. Nigel, I may need some of your expertise here. It looks like there's a consistent problem with svn checkouts.

"git clone" operations seem to have been successful, so it probably isn't a matter of GitHub being down. Especially since the svn checkout of geostd from Sourceforge also failed.

Do you know if your system has problems with svn? Our svn checkouts generally take this form: " svn co https://github.com/rlabduke/MolProbity.git/trunk molprobity --non-interactive --trust-server-cert " Is there perhaps a security issue with the --trust-server-cert flag?

I believe that the cci machines at Berkeley are under maintenance until Sunday, so there are other reasons the script won't work until then.

Good luck,

-Christopher Williams

---Richardson Lab, Duke University

On Fri, Aug 16, 2019 at 5:45 PM Charitha Belluru Shetty < [email protected]> wrote:

Hi Christopher,

I ran the installer script twice and this is what I got…

*When I ran it first time, only the modules directory was created*

bash-4.2$ *. install_via_bootstrap.sh 10*

++++++++++ creating build directories ...

svn: E000110: Unable to connect to a repository at URL 'svn:// svn.code.sf.net/p/geostd/code/trunk'

svn: E000110: Can't read from connection: Connection timed out

svn: E175002: Unable to connect to a repository at URL ' https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotamer... '

svn: E175002: OPTIONS of ' https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotamer...': SSL handshake failed: SSL socket read failed (https://github.com)

svn: E175002: Unable to connect to a repository at URL ' https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramacha... '

svn: E175002: OPTIONS of ' https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramacha...': SSL handshake failed: SSL socket read failed (https://github.com)

svn: E175002: Unable to connect to a repository at URL ' https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam_... '

svn: E175002: OPTIONS of ' https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam_...': SSL handshake failed: SSL socket read failed (https://github.com)

svn: E175002: Unable to connect to a repository at URL ' https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstrap... '

svn: E175002: OPTIONS of ' https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstrap...': SSL handshake failed: SSL socket read failed (https://github.com)

python: can't open file 'bootstrap.py': [Errno 2] No such file or directory

-bash: build/setpaths.sh: No such file or directory

python: can't open file 'modules/chem_data/cablam_data/rebuild_cablam_cache.py': [Errno 2] No such file or directory

++++++++++ MolProbity configure.sh finished.

++++++++++ Run molprobity/setup.sh to complete installation.

-bash-4.2$

-bash-4.2$ pwd

/hpc/apps/current/molprobity/v4.4.app

-bash-4.2$ ls -l

total 31

*-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh*

*drwxr-sr-x 3 cbs72396 appmgmt 3 Aug 15 17:58 modules*

*Second time when I ran..bootstap.py and bootstrap.pyc was crated and the modules directory…*

-bash-4.2$ *. install_via_bootstrap.sh 4*

++++++++++ creating build directories ...

svn: E000110: Unable to connect to a repository at URL 'svn:// svn.code.sf.net/p/geostd/code/trunk'

svn: E000110: Can't read from connection: Connection timed out

Performing actions: hot update base build

Installing base packages using:

python modules/cctbx_project/libtbx/auto_build/install_conda.py --builder=molprobity --install_conda

===== Downloading http://cci.lbl.gov/repositories/annlib.gz: 0.5 MB

[0%.........20%.........40%.........60%.........80%.........100%]

===== Running in modules: extracting files from annlib.gz

===== Downloading http://cci.lbl.gov/repositories/scons.gz: 0.6 MB

[0%.........20%.........40%.........60%.........80%.........100%]

===== Running in modules: extracting files from scons.gz

===== Downloading http://cci.lbl.gov/repositories/ccp4io.gz: 1.4 MB

[0%.........20%.........40%.........60%.........80%.........100%]

===== Running in modules: extracting files from ccp4io.gz

===== Running in modules: git clone --recursive https://github.com/cctbx/boost.git boost --progress --verbose

Cloning into 'boost'...

POST git-upload-pack (942 bytes)

remote: Enumerating objects: 27664, done.

remote: Total 27664 (delta 0), reused 0 (delta 0), pack-reused 27664

Receiving objects: 100% (27664/27664), 20.47 MiB | 14.72 MiB/s, done.

Resolving deltas: 100% (15913/15913), done.

Checking out files: 100% (14245/14245), done.

setting branch master to rebase

===== Running in modules/boost: git rev-parse HEAD

72edfa007c73dd3dd01f5530205f7ca14cda7420

===== Running in modules: git clone --recursive https://github.com/yayahjb/cbflib.git cbflib --progress --verbose

Cloning into 'cbflib'...

POST git-upload-pack (gzip 2442 to 1233 bytes)

remote: Enumerating objects: 7463, done.

remote: Total 7463 (delta 0), reused 0 (delta 0), pack-reused 7463

Receiving objects: 100% (7463/7463), 24.84 MiB | 13.21 MiB/s, done.

Resolving deltas: 100% (5380/5380), done.

setting branch master to rebase

===== Running in modules/cbflib: git rev-parse HEAD

611f21bbef81c5104954aaab9b72e4e55ec3e70d

===== Running in modules: git clone --recursive https://github.com/cctbx/cctbx_project.git cctbx_project --progress --verbose

Cloning into 'cctbx_project'...

POST git-upload-pack (gzip 1842 to 958 bytes)

remote: Enumerating objects: 61, done.

remote: Counting objects: 100% (61/61), done.

remote: Compressing objects: 100% (52/52), done.

remote: Total 243691 (delta 14), reused 22 (delta 9), pack-reused 243630

Receiving objects: 100% (243691/243691), 91.05 MiB | 14.77 MiB/s, done.

Resolving deltas: 100% (192566/192566), done.

Checking out files: 100% (6173/6173), done.

setting branch master to rebase

===== Running in modules/cctbx_project: git rev-parse HEAD

bd3139c85312f5f43009e1eb31baa34f41734fbb

===== Downloading http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz: 203.9 kB

[0%.........20%.........40%.........60%.........80%.........100%]

===== Running in modules: extracting files from ccp4io_adaptbx.gz

===== Running in modules: git clone --recursive https://github.com/cctbx/annlib_adaptbx.git annlib_adaptbx --progress --verbose

Cloning into 'annlib_adaptbx'...

POST git-upload-pack (842 bytes)

remote: Enumerating objects: 175, done.

remote: Total 175 (delta 0), reused 0 (delta 0), pack-reused 175

Receiving objects: 100% (175/175), 162.09 KiB | 0 bytes/s, done.

Resolving deltas: 100% (77/77), done.

setting branch master to rebase

===== Running in modules/annlib_adaptbx: git rev-parse HEAD

3ca66b2dd77eacd7524f915fce0705ac0764b46f

===== Downloading http://cci.lbl.gov/repositories/tntbx.gz: 38.0 kB

[0%.........20%.........40%.........60%.........80%.........100%]

===== Running in modules: extracting files from tntbx.gz

===== Running in .: svn co https://github.com/rlabduke/MolProbity.git/trunk molprobity --non-interactive --trust-server-cert

svn: E175002: Unable to connect to a repository at URL ' https://github.com/rlabduke/MolProbity.git/trunk'

svn: E175002: OPTIONS of 'https://github.com/rlabduke/MolProbity.git/trunk': SSL handshake failed: SSL socket read failed (https://github.com)

Process failed with return code 1

-bash: build/setpaths.sh: No such file or directory

Traceback (most recent call last):

File "modules/chem_data/cablam_data/rebuild_cablam_cache.py", line 2, in <module>

import libtbx.load_env

ImportError: No module named libtbx.load_env

++++++++++ MolProbity configure.sh finished.

++++++++++ Run molprobity/setup.sh to complete installation.

-bash-4.2$

-bash-4.2$

*-bash-4.2$ ls -l*

*total 131*

*-rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py*

*-rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc*

*-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh*

*drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules*

Best Regards,

Charitha Shetty

*From:* Christopher Williams *Sent:* Wednesday, August 14, 2019 2:23 PM *To:* Robert Nolte *Cc:* Nigel Moriarty ; Charitha Belluru Shetty < [email protected]>; [email protected] *Subject:* Re: Molprobity / CCTBX incompatibility

*EXTERNAL*

Hi All,

Okay looks like the new installer works. It uses the conda mode of the cctbx bootstrap builder for everything except chem_data, which it builds on its own.

Get the new installer from our GitHub here:

svn --quiet --non-interactive --trust-server-cert export https://github.com/rlabduke/MolProbity.git/trunk/install_via_bootstrap.sh

Place it in the dir where you want to install MolProbity, then run it.

. install_via_bootstrap.sh

The script optionally accepts a single integer argument to set the number of processors that the bootstrap builder will use.

. install_via_bootstrap.sh 4

When this is complete, cd to the molprobity dir it created and run setup.sh, as usual.

Good luck,

-Christopher Williams

---Richardson Lab, Duke University

On Wed, Aug 14, 2019 at 1:33 PM Christopher Williams < [email protected]> wrote:

Hi Bob,

I am currently doing one more test build to make sure that the new installer works. It looks promising.

Regards,

-Christopher Williams

---Richardson Lab, Duke University

On Wed, Aug 14, 2019 at 11:17 AM Robert Nolte wrote:

Folks,

Any progress on sorting out our issue, or cleaning up the installer?

Bob

*From:* Christopher Williams *Sent:* Monday, August 12, 2019 7:48 PM *To:* Nigel Moriarty *Cc:* Robert Nolte ; Charitha Belluru Shetty < [email protected]>; [email protected] *Subject:* Re: Molprobity / CCTBX incompatibility

*EXTERNAL*

The dispatcher should be using both phenix.reduce and molprobity.reduce interchangeably in all cases. Ditto for all the validations that MolProbity runs like phenix.rotalyze/molprobity.rotalyze.

My current install of MolProbity is successfully accessing Reduce via phenix.reduce, so I don't *think* this is the issue.

-Christopher Williams

---Richardson Lab, Duke University

On Mon, Aug 12, 2019 at 6:07 PM Nigel Moriarty wrote:

But maybe the installation of cctbx has molprobity.reduce and not phenix.reduce so if that is the case we can change the script to look for molprobity.reduce instead of phenix.reduce.

Cheers

Nigel

---

Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte wrote:

According to the log file when I just tried to run it, it is phenix.reduce that it can’t find.

Bob

*From:* Nigel Moriarty *Sent:* Monday, August 12, 2019 5:55 PM *To:* Robert Nolte *Cc:* Charitha Belluru Shetty ; Christopher Williams ; [email protected] *Subject:* Re: Molprobity / CCTBX incompatibility

*EXTERNAL*

I'm just trying to find out if, at the command line, whether it is phenix.reduce or molprobity.reduce. Charitha just needs to type one or the other to see what happens.

Cheers

Nigel

---

Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte wrote:

Nigel,

Currently it is not running. This was working from the scratch install last week. I am not sure what is going on now.

Bob

*From:* Nigel Moriarty *Sent:* Monday, August 12, 2019 4:52 PM *To:* Charitha Belluru Shetty *Cc:* Christopher Williams ; [email protected]; Robert Nolte *Subject:* Re: Molprobity / CCTBX incompatibility

*EXTERNAL*

Does molprobity.reduce run?

Cheers

Nigel

---

Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < [email protected]> wrote:

Hi Nigel,

I hit the send button too soon..Ignore my previous email 😊

-bash-4.2$ source setpaths.sh

-bash-4.2$

-bash-4.2$ env |grep -i reduce

-bash-4.2$

So the “setpath.sh” has the below contents…

$ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh

# THIS IS AN AUTOMATICALLY GENERATED FILE.

# DO NOT EDIT! CHANGES WILL BE LOST.

ocwd="`pwd`"

if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then

cd "$LIBTBX_BUILD_RELOCATION_HINT"

LIBTBX_BUILD_RELOCATION_HINT=

export LIBTBX_BUILD_RELOCATION_HINT

elif [ -n "$BASH_SOURCE" ]; then

LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"`

cd "$LIBTBX_BUILD"

else

cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build"

fi

LIBTBX_BUILD=`pwd -P`

export LIBTBX_BUILD

LIBTBX_OPATH="$PATH"

export LIBTBX_OPATH

PATH="$LIBTBX_BUILD/bin:$PATH"

export PATH

cd "$ocwd"

ocwd=

alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\""

alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\""

if [ -n "$LIBTBX_OPATH" ]; then

LIBTBX_TMPVAL="$LIBTBX_OPATH"

else

LIBTBX_TMPVAL=

fi

export LIBTBX_TMPVAL

PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < /dev/null`

export PATH

if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi

LIBTBX_TMPVAL=

LIBTBX_OPATH=

LIBTBX_BUILD=

Best Regards,

Charitha Shetty

*From:* Nigel Moriarty *Sent:* Monday, August 12, 2019 4:08 PM *To:* Charitha Belluru Shetty *Cc:* Christopher Williams ; [email protected]; Robert Nolte *Subject:* Re: Molprobity / CCTBX incompatibility

*EXTERNAL*

Once you source the setpaths.sh file in the build directory do you have phenix.reduce or molprobity.reduce?

Cheers

Nigel

---

Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging

Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < [email protected]> wrote:

Hi Christopher/ Nigel,

Thank you for your quick reply.

The build process was completed without any error. Pasting few of the lines from it…

===== Running in build: rebuild rotarama

Processing data files in "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data":

rota8000-cys.data -> rota8000-cys.pickle: converting ... done.

rota8000-asp.data -> rota8000-asp.pickle: converting ... done.

rota8000-ser.data -> rota8000-ser.pickle: converting ... done.

rota8000-gln.data -> rota8000-gln.pickle: converting ... done.

rota8000-ile.data -> rota8000-ile.pickle: converting ... done.

rota8000-pro.data -> rota8000-pro.pickle: converting ... done.

rota8000-lys.data -> rota8000-lys.pickle: converting ... done.

rota8000-thr.data -> rota8000-thr.pickle: converting ... done.

rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done.

rota8000-glu.data -> rota8000-glu.pickle: converting ... done.

rota8000-met.data -> rota8000-met.pickle: converting ... done.

rota8000-his.data -> rota8000-his.pickle: converting ... done.

rota8000-leu.data -> rota8000-leu.pickle: converting ... done.

rota8000-arg.data -> rota8000-arg.pickle: converting ... done.

rota8000-trp.data -> rota8000-trp.pickle: converting ... done.

rota8000-asn.data -> rota8000-asn.pickle: converting ... done.

rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date.

rota8000-val.data -> rota8000-val.pickle: converting ... done.

Processing data files in "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data":

rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting ... done.

rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done.

rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done.

rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: converting ... done.

rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done.

rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... done.

u+s,u,s: 10.06 9.83 0.23

===== Running in .: libtbx.refresh

Python: 2.7.16 "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7"

Compiler: default

Build mode: release

Warning level: 0

Precompiled Headers: False

Static libraries: False

Static exe: False

Scan Boost headers: False

Write full flex_fwd.h files: False

Build Boost.Python extensions: True

Define BOOST_PYTHON_NO_PY_SIGNATURES: False

Define BOOST_PYTHON_BOOL_INT_STRICT: True

Enable OpenMP if possible: False

Boost threads enabled: True

Enable CUDA: False

Use conda: False

Use opt_resources if available: False

Use environment flags: False

Enable C++11: False

Python3 migration warning policy: None

command_version_suffix: None

Relocatable paths anchored at: /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build

Top-down list of all modules involved:

mmtbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx"

iotbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx"

ccp4io+adaptbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io"

"/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx"

smtbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx"

ucif "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif"

cctbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx"

scitbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx"

fable "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable"

omptbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx"

boost+adaptbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost"

"/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx"

tbxx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx"

chiltbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx"

libtbx "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx"

Creating files in build directory: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build"

dispatcher_include_template.sh

dispatcher_head.sh

setpaths.sh

setpaths.csh

setpaths_all.sh

setpaths_all.csh

setpaths_debug.sh

unsetpaths.sh

setpaths_debug.csh

unsetpaths.csh

SConstruct

Makefile

run_tests.csh

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py"

Generating C++ header files in:

"/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family"

Generating C++ files in:

"/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python"

Using fable to convert scitbx/lbfgs.f

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py"

Generating C++ files in:

"/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx"

Generating C++ files in:

"/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py"

Generating C++ files in:

"/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py"

Using fable to convert iotbx/pdb/hybrid_36_f.f

Writing: iotbx/pdb/hybrid_36_fem.cpp

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py"

Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev"

Regenerating module files in /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base

/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, could not regenerate pango files

/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not present, could not regenerate gdk-pixbuf.loaders

/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, could not rebuild fonts

generating index.theme file

Done.

*Bootstrap success: build*

*++++++++++ MolProbity configure.sh finished.*

[tm375568@uptus060-3 MolProbity]$ ./setup.sh

++++++++++ creating directories ...

++++++++++ setting permisions ...

*Couldn't get a file descriptor referring to the console **à I assume this can be ignored. *

[tm375568@uptus060-3 MolProbity]$

Best Regards,

Charitha Shetty

*From:* Christopher Williams *Sent:* Monday, August 12, 2019 3:34 PM *To:* Charitha Belluru Shetty *Cc:* Nigel Moriarty ([email protected]) ; [email protected]; Robert Nolte *Subject:* Re: Molprobity / CCTBX incompatibility

*EXTERNAL*

Hmm. It looks like Reduce and/or Probe has failed to install correctly. Most likely an early call to Reduce has resulted in an empty file, which is then passed into other programs, resulting in error messages.

The configure script ran a build process. Do you know if that process finished successfully or if it ended with errors? If the build exited early, it may have never reached the part where Reduce gets compiled. Some dependencies have changed, and I have been having trouble with my own builds lately.

It is also possible that there was just a network hiccup that prevented something from downloading correctly, and a second attempt will work.

I am working on a new configure/install script for more consistent handling of dependencies. Hopefully it will be ready in about a day.

Good luck,

-Christopher Williams

---Richardson Lab, Duke University

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