Showing posts with label debian jessie. Show all posts
Showing posts with label debian jessie. Show all posts

20 January 2016

628. Very briefly: Crystalmaker in debian jessie with wine-staging (1.9)

Update:
 I am seeing consistent crashes with files containing multiple structures (e.g. multi-xyz or multi-cif files). They open fine in a virtualbox instance of crystalmaker.

The terminal shows
fixme:shell:check_flags Unsupported flags: 2414
Before buying crystalmaker, make sure to try it extensively first as there is a free demo version available.

Original post:
This is a brief and somewhat incomplete post.
I recently bought a crystalmaker license, knowing that it had no support under linux. I figured that I'd live with running it in an XP VM. My allergies to all things windows made me very unhappy with that solution, however.

So I tried to install crystalmaker using wine in jessie (1.6.2) and the current (1.50.1) version of Crossover. The installation worked fine for both, but running the software lead to crashes.

I then installed the winehq-staging version (1.9):
sudo apt-get install apt-transport-https
wget https://dl.winehq.org/wine-builds/Release.key
sudo apt-key add Release.key

I edited /etc/apt/sources.list
deb https://dl.winehq.org/wine-builds/debian/ jessie main
sudo apt-get update
sudo sudo apt-get install winehq-staging

Same issue.

I then finally actually read the crash message, which mentioned that
wine: Unimplemented function msvcp120.dll.?_Throw_C_error@std@@YAXH@Z called at address 0x7b83a70c (thread 004e), starting debugger...
That lead me to install vcrun2013 using winetricks:
winetricks -q vcrun2013 gdiplus

Crystalmaker now works perfectly (as far as I can see) under wine. Saving graphics as PNG works too. I haven't tried anything else as I'm not familiar with crystalmaker.



[NOTE: by running WINEPREFIX=~/.cxoffice/crystalmaker winetricks vcrun2013 I later got it to work in crossover. I haven't tried wine 1.6.2 again.]

[Note 2: gdiplus is needed to fix messages of the type
fixme:gdiplus:Gdip<...> graphics object has no HDC]

28 July 2015

618. Modifying ECCE to work with slurm

UPDATE: ecce stops monitoring the job after 10-20 seconds. The job continues fine though. Working on fixing the monitoring issue. This message will be removed once that's fixed. It was due to $q needing to be lowercase (i.e. 'slurm', not 'Slurm') in eccejobmonitor.



Sun Gridengine has been removed from debian jessie (it's in wheezy and sid). This has given me a good excuse to explore setting up SLURM on my debian cluster. So I did: http://verahill.blogspot.com.au/2015/07/617-slurm-on-debian-jessie-and.html

My setup is very simple, with each node having it's own working directory that they export via NFS to the main node. Also, I never run jobs across several nodes. Because of that, each node has it's own queue. Not how beowulf clusters were supposed to work, but it's the best solution for me (e.g. ROCKS does the opposite -- exports the user dir from the main node, but that makes reading and writing slow where it counts i.e. on the work nodes).

I've currently got this slurm.conf:
ControlMachine=beryllium ControlAddr=192.168.1.1 MpiDefault=none ProctrackType=proctrack/pgid ReturnToService=2 SlurmctldPidFile=/var/run/slurm-llnl/slurmctld.pid SlurmdPidFile=/var/run/slurm-llnl/slurmd.pid SlurmdSpoolDir=/var/lib/slurm/slurmd SlurmUser=slurm StateSaveLocation=/var/lib/slurm/slurmctld SwitchType=switch/none TaskPlugin=task/none FastSchedule=1 SchedulerType=sched/backfill SelectType=select/linear AccountingStorageType=accounting_storage/filetxt AccountingStorageLoc=/var/log/slurm/accounting ClusterName=rupert JobAcctGatherType=jobacct_gather/none SlurmctldLogFile=/var/log/slurm/slurmctld.log SlurmdLogFile=/var/log/slurm/slurmd.log NodeName=beryllium NodeAddr=192.168.1.1 NodeName=neon NodeAddr=192.168.1.120 state=unknown NodeName=tantalum NodeAddr=192.168.1.150 state=unknown NodeName=magnesium NodeAddr=192.168.1.200 state=unknown NodeName=carbon NodeAddr=192.168.1.190 state=unknown NodeName=oxygen NodeAddr=192.168.1.180 state=unknown PartitionName=All Nodes=neon,beryllium,tantalum,oxygen,magnesium,carbon default=yes maxtime=infinite state=up PartitionName=mpi4 Nodes=tantalum maxtime=infinite state=up PartitionName=mpi12 Nodes=carbon maxtime=infinite state=up PartitionName=mpi8 Nodes=neon maxtime=infinite state=up PartitionName=mpix8 Nodes=oxygen maxtime=infinite state=up PartitionName=mpix12 Nodes=magnesium maxtime=infinite state=up PartitionName=mpi1 Nodes=beryllium maxtime=infinite state=up
and sinfo returns
PARTITION AVAIL TIMELIMIT NODES STATE NODELIST All* up infinite 6 idle beryllium,carbon,magnesium,neon,oxygen,tantalum mpi4 up infinite 1 idle tantalum mpi12 up infinite 1 idle carbon mpi8 up infinite 1 idle neon mpix8 up infinite 1 idle oxygen mpix12 up infinite 1 idle magnesium mpi1 up infinite 1 idle beryllium

The first step was to figure out what files to edit:

grep -rs "qsub"
apps/siteconfig/QueueManagers:SGE|submitCommand: qsub ##script##
grep -rs "SGE"
apps/scripts/eccejobmonitor: &MsgSendUp("SGE job id '$id' in state '$state'"); [..] apps/siteconfig/Queues:magnesium|queueMgrName: SGE

Here are the files I edited:

apps/siteconfig/QueueManagers:
12 QueueManagers: LoadLeveler \ 13 Maui \ 14 EASY \ 15 PBS \ 16 LSF \ 17 Moab \ 18 SGE \ 19 Shell\ 20 Slurm
185 Shell|jobIdParseExpression: \ [0-9]+ 186 187 ############################################################################### 188 # SLURM 189 # Simple Linux Utility for Resource Management 190 # 191 # 192 Slurm|submitCommand: sbatch ##script## 193 Slurm|cancelCommand: scancel ##id## 194 Slurm|queryJobCommand: squeue 195 Slurm|queryMachineCommand: sinfo -p ##queue## 196 Slurm|queryQueueCommand: squeue -a 197 Slurm|queryDiskUsageCommand: df -k 198 Slurm|jobIdParseExpression: .* 199 Slurm|jobIdParseLeadingText: job
apps/scripts/eccejobmonitor:
2124 LogMsg "Globus status from eccejobstore: $state"; 2125 } 2126 elsif ($q eq 'slurm') 2127 { 2128 $cmd = "squeue 2>&1"; 2129 if (open(QUERY, "$cmd |")) 2130 { 2131 $gotState = 0; 2132 while () 2133 { 2134 LogMsg "JobCheck: Slurm qstat line: $_"; 2135 if (/^\s*$id/) 2136 { 2137 my $state = (split)[5]; 2138 2139 &MsgSendUp("Slurm job id '$id' in state '$state'"); 2140 2141 if (grep {$state eq $_} qw{R 2142 t}) 2143 { 2144 $status = $JOB_STATE_RUNNING; 2145 } 2146 elsif (grep {$state eq $_} qw{PD}) 2147 { 2148 $status = $JOB_STATE_PENDING; 2149 } 2150 $gotState = 1; 2151 last; 2152 } 2153 } 2154 if ($gotState == 0) 2155 { 2156 if ($gJobCheckState != $JOB_STATE_NONE) 2157 { 2158 $status = $JOB_STATE_DONE; 2159 } 2160 } 2161 close QUERY;

Next set up a new machine (or queue) using ecce -admin. Set up a queue -- you won't be able to select Slurm, so select e.g. PBS. Edit the apps/siteconfig/CONFIG.machinename file to e.g.
1 NWChem: /opt/nwchem/Nwchem/bin/LINUX64/nwchem 2 Gaussian-03: /opt/gaussian/g09d/g09/g09 3 perlPath: /usr/bin/ 4 qmgrPath: /usr/bin/ 5 xappsPath: /usr/bin/ 6 7 Slurm { 8 #!/bin/csh 9 #SBATCH -p mpi8 10 #SBATCH --time=$walltime 11 #SBATCH --output=slurm.out 12 #SBATCH --job-name=$submitFile 13 } 14 15 NWChemEnvironment { 16 PYTHONPATH /opt/nwchem/Nwchem/contrib/python 17 } 18 19 NWChemFilesToRemove{ core *.aoints.* *.gridpts.* } 20 21 NWChemCommand { 22 setenv PATH "/bin:/usr/bin:/sbin:/usr/sbin" 23 setenv LD_LIBRARY_PATH "/usr/lib/openmpi/lib:/opt/openblas/lib:/opt/acml/acml5.3.1/gfortran64_fma4_int64/lib:/opt/acml/acml5.3.1/gfortran64_int64/lib:/opt/intel/mkl/lib/intel64" 24 hostname 25 mpirun -n $totalprocs /opt/nwchem/Nwchem/bin/LINUX64/nwchem $infile > $outfile 26 } 27 28 Gaussian-03FilesToRemove{ core *.rwf } 29 30 Gaussian-03Command{ 31 set path = ( /opt/nbo6/bin $path ) 32 setenv GAUSS_SCRDIR /home/me/scratch 33 setenv GAUSS_EXEDIR /opt/gaussian/g09d/g09/bsd:/opt/gaussian/g09d/g09/local:/opt/gaussian/g09d/g09/extras:/opt/gaussian/g09d/g09 34 /opt/gaussian/g09d/g09/g09< $infile > $outfile 35 echo 0 36 } 37 38 Wrapup{ 39 dmesg|tail 40 find ~/scratch/* -name "*" -user me|xargs -I {} rm {} -rf 41 }
Next, edit apps/siteconfig/Queues -- in my case the machine I created is called neon-slurm:
neon-slurm|queueMgrName: Slurm neon-slurm|queueMgrVersion: 2.0~ neon-slurm|prefFile: neon-slurm.Q
And that's all. You should now be able to submit jobs via slurm. There's obviously a lot more than can be done and configured with SLURM, but this was enough to get me up and running, so that I'm now 'future-proofed' in case SGE never comes back into debian stable.

And here's what it looks like when my ecce-submitted jobs are running:

squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 30 mpi8 In_monom me PD 0:00 1 (Resources) 29 mpi8 b_monome me R 16:12 1 neon 31 mpix12 tl_dimer me R 34:28 1 magnesium

617. SLURM on debian jessie (and compiling Jürgen Rinas' sinfo)

Two issues:
* Sun GridEngine (now Oracle GridEngine) is missing from Debian Jessie. I need a queue manager for my cluster. For now the wheezy package runs fine in debian jessie, but I'd be happier with a supported solution. SLURM is a good alternative here, and I've used it at the TACC.

* SLURM conflicts with Jürgen Rinas' sinfo package, which I use to keep an eye on my cluster. Until this has been resolved, I'll compile and use my own version of sinfo -- basically, I'll rename sinfo and sinfod to sinfo_jr and sinfod_jr. I can't live without sinfo.



Compiling sinfo
mkdir ~/tmp/sinfo -p
cd ~/tmp/sinfo
sudo apt-get install build-essential
sudo apt-get autoremove sinfo 
apt-get source sinfo
cd sinfo-0.0.47/
vim debian/rules 

Change
16 dh_auto_configure -- --enable-SIMPLE_USER_CACHE --enable-CPUNO_ADJUST 21 rm $(CURDIR)/debian/sinfo/usr/bin/sshallsinfo 22 rm $(CURDIR)/debian/sinfo/usr/share/man/man1/sshallsinfo.1 25 rm $(CURDIR)/debian/sinfo/usr/lib/*/sinfo/*.la 37 chmod 755 $(CURDIR)/debian/sinfo/usr/share/sinfo/sinfo.pl.cgi
to
16 dh_auto_configure -- --enable-SIMPLE_USER_CACHE --enable-CPUNO_ADJUST --program-suffix=_jr 21 rm $(CURDIR)/debian/sinfojr/usr/bin/sshallsinfo_jr 22 rm $(CURDIR)/debian/sinfojr/usr/share/man/man1/sshallsinfo_jr.1 25 rm $(CURDIR)/debian/sinfojr/usr/lib/*/sinfo/*.la 37 chmod 755 $(CURDIR)/cgi/sinfo.pl.cgi
That's jr for Jürgen Rinas.

Then edit debian/control and change
12 Package: sinfo
15 Conflicts: slurm-client, slurm-llnl (<< 14.03.8-1)
to
12 Package: sinfojr
15 Conflicts: 
Build:
dpkg-buildpackage -us -uc
cd ../
sudo dpkg -i sinfo_0.0.47-3_amd64.deb

I launch sinfodjr at boot by putting the following in /etc/rc.local:
su verahill -c '/usr/sbin/sinfodjr --bcast 192.168.1.255' &

SLURM:
I had a look at this post: https://paolobertasi.wordpress.com/2011/05/24/how-to-install-slurm-on-debian/

It looked to easy to be true.

Here's what I ended up doing:

On the MASTER node:
sudo apt-get install slurm-wlm slurmctld slurmd
[..] Generating a pseudo-random key using /dev/urandom completed. Please refer to /usr/share/doc/munge/README.Debian for instructions to generate more secure key. Setting up slurm-client (14.03.9-5) ... Setting up slurm-wlm-basic-plugins (14.03.9-5) ... Setting up slurmd (14.03.9-5) ... Setting up slurmctld (14.03.9-5) ... Setting up slurm-wlm (14.03.9-5) ... [..]
open file:///usr/share/doc/slurmctld/slurm-wlm-configurator.easy.html
# slurm.conf file generated by configurator easy.html. # Put this file on all nodes of your cluster. # See the slurm.conf man page for more information. # ControlMachine=beryllium ControlAddr=192.168.1.1 # #MailProg=/bin/mail MpiDefault=none #MpiParams=ports=#-# ProctrackType=proctrack/pgid ReturnToService=2 SlurmctldPidFile=/var/run/slurm-llnl/slurmctld.pid #SlurmctldPort=6817 SlurmdPidFile=/var/run/slurm-llnl/slurmd.pid #SlurmdPort=6818 SlurmdSpoolDir=/var/lib/slurm/slurmd SlurmUser=slurm #SlurmdUser=root StateSaveLocation=/var/lib/slurm/slurmctld SwitchType=switch/none TaskPlugin=task/none # # # TIMERS #KillWait=30 #MinJobAge=300 #SlurmctldTimeout=120 #SlurmdTimeout=300 # # # SCHEDULING FastSchedule=1 SchedulerType=sched/backfill #SchedulerPort=7321 SelectType=select/linear # # # LOGGING AND ACCOUNTING AccountingStorageType=accounting_storage/none ClusterName=rupert #JobAcctGatherFrequency=30 JobAcctGatherType=jobacct_gather/none #SlurmctldDebug=3 SlurmctldLogFile=/var/log/slurm/slurmctld.log #SlurmdDebug=3 SlurmdLogFile=/var/log/slurm/slurmd.log # # # COMPUTE NODES NodeName=beryllium NodeAddr=192.168.1.1 NodeName=neon NodeAddr=192.168.1.120 PartitionName=All Nodes=beryllium,neon
Copy the above block to /etc/slurm-llnl/slurm.conf

Note the lack of spaces between beryllium and neon in the Nodes= directive.
scontrol show daemons
slurmctld
sudo /usr/sbin/create-munge-key
The munge key /etc/munge/munge.key already exists Do you want to overwrite it? (y/N) y Generating a pseudo-random key using /dev/urandom completed.
sudo systemctl enable slurmctld.service
sudo ln -s /var/lib/slurm-llnl /var/lib/slurm
sudo systemctl start slurmctld.service
sudo systemctl status slurmctld.service 
● slurmctld.service - Slurm controller daemon Loaded: loaded (/lib/systemd/system/slurmctld.service; enabled) Active: active (running) since Tue 2015-07-21 11:16:18 AEST; 40s ago Process: 19958 ExecStart=/usr/sbin/slurmctld $SLURMCTLD_OPTIONS (code=exited, status=0/SUCCESS) Main PID: 19960 (slurmctld) CGroup: /system.slice/slurmctld.service └─19960 /usr/sbin/slurmctld
sudo systemctl status munge.service
● munge.service - MUNGE authentication service Loaded: loaded (/lib/systemd/system/munge.service; disabled) Active: active (running) since Wed 2015-07-08 00:11:18 AEST; 1 weeks 6 days ago Docs: man:munged(8) Main PID: 25986 (munged) CGroup: /system.slice/munge.service └─25986 /usr/sbin/munged
Also, add yourself to the group slurm and chmod g+r /var/log/slurm/accounting.

On neon (and later on each node): 
Install slurmd and slurm-client as shown below, then copy the /etc/munge/munge.key from the master node to the execute node. Do the same with /etc/slurm-llnl/slurm.conf. Then enable and restart the services.

sudo apt-get install slurmd slurm-client
sudo ln -s /var/lib/slurm-llnl /var/lib/slurm
sudo systemctl enable slurmd.service
sudo systemctl restart slurmd.service
sudo systemctl enable munge.service
sudo systemctl restart munge.service
sudo systemctl status slurmd.service

On the main host (beryllium) I checked that everything was well:

sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
All          up   infinite      1  idle* beryllium, neon

26 July 2015

616. SIESTA on debian jessie with debian blacs, scalapack and SIESTA blas

Three posts showing slightly different ways of building SIESTA on debian may seem a bit excessive, but I figured I'd do a post on a simple 'bullet-proof' way of building SIESTA on debian jessie.

For ACML, see http://verahill.blogspot.com.au/2015/07/614-siesta-with-mpi-on-debian-jessie.html
For MKL (not all MKL versions work using that post): http://verahill.blogspot.com.au/2015/07/615-siesta-on-debian-jessie-with-intel.html

See those posts for detailed build instructions. I'll only give you the arch.make here -- for the rest, see either of the above posts.

I've got a node with intel mkl 2013.sp1.3.174 which hasn't got the blacs openmpi libs, so I ended up building SIESTA with the SIESTA BLAS and LAPACK libraries, and using the debian BLACS and SCALAPACK libs.

Install the libs with
sudo apt-get install libblacs-openmpi1 libopenmpi-dev libscalapack-openmpi1 libblacs-mpi-dev libscalapack-mpi-dev


Here's the arch.make:
# # This file is part of the SIESTA package. # # Copyright (c) Fundacion General Universidad Autonoma de Madrid: # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal # and J.M.Soler, 1996- . # # Use of this software constitutes agreement with the full conditions # given in the SIESTA license, as signed by all legitimate users. # .SUFFIXES: .SUFFIXES: .f .F .o .a .f90 .F90 SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown FPP= FPP_OUTPUT= FC=mpif90 RANLIB=ranlib SYS=nag SP_KIND=4 DP_KIND=8 KINDS=$(SP_KIND) $(DP_KIND) FFLAGS=-g -O2 FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT LDFLAGS= ARFLAGS_EXTRA= FCFLAGS_fixed_f= FCFLAGS_free_f90= FPPFLAGS_fixed_F= FPPFLAGS_free_F90= BLAS_LIBS= LAPACK_LIBS= BLACS_LIBS=-L/usr/lib -lblacs-openmpi SCALAPACK_LIBS=-L/usr/lib -lscalapack-openmpi COMP_LIBS=dc_lapack.a liblapack.a libblas.a NETCDF_LIBS= NETCDF_INTERFACE= MPI_LIBS=-L/usr/lib/openmpi/lib -lmpi -lmpi_f90 -lmpi_f77 LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS) $(MPI_LIBS) -lpthread #SIESTA needs an F90 interface to MPI #This will give you SIESTA's own implementation #If your compiler vendor offers an alternative, you may change #to it here. MPI_INTERFACE=libmpi_f90.a MPI_INCLUDE=. #Dependency rules are created by autoconf according to whether #discrete preprocessing is necessary or not. .F.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $< .F90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $< .f.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $< .f90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
At some point in the future, when my nodes are free, I might do a bit of basic performance testing using the different versions.

25 July 2015

615. SIESTA on debian jessie with intel mkl and ifort

It's pretty similar to what I described in http://verahill.blogspot.com.au/2015/07/614-siesta-with-mpi-on-debian-jessie.html, with the main differences being the SCALAPACK, FC, BLACS and BLAS settings in arch.make

I presume that (the sadly no longer free for non-US academics) MKL was set up as shown here: http://verahill.blogspot.com.au/2013/06/465-intel-mkl-math-kernel-library-on.html

I haven't run all the tests on the build yet, but most of the ones that I tried worked, with the exception of the benzene test which came out with "Failure to converge standard eigenproblem", which is described here: http://departments.icmab.es/leem/siesta/Documentation/Manuals/manual-2.0/node47.html and isn't due to the build parameters.

NOTE: this doesn't work on mkl version 2013.sp1.3.174 as the blacs openmpi lib is missing. It does work on 2013.3.163, which is the version I used below. I have no idea why the libraries supplied with mkl are so different.

Follow
sudo apt-get install libopenmpi-dev
sudo mkdir /opt/siesta
sudo chown $USER /opt/siesta
cd /opt/siesta
wget http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz
tar xvf siesta-3.2-pl-5.tgz
cd siesta-3.2-pl-5/Obj
sh ../Src/obj_setup.sh
../Src/./configure --enable-mpi

Edit arch.make:
# # This file is part of the SIESTA package. # # Copyright (c) Fundacion General Universidad Autonoma de Madrid: # E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal # and J.M.Soler, 1996- . # # Use of this software constitutes agreement with the full conditions # given in the SIESTA license, as signed by all legitimate users. # .SUFFIXES: .SUFFIXES: .f .F .o .a .f90 .F90 SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown FPP= FPP_OUTPUT= FC=ifort RANLIB=ranlib SYS=nag SP_KIND=4 DP_KIND=8 KINDS=$(SP_KIND) $(DP_KIND) FFLAGS=-g -O2 FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT LDFLAGS= ARFLAGS_EXTRA= FCFLAGS_fixed_f= FCFLAGS_free_f90= FPPFLAGS_fixed_F= FPPFLAGS_free_F90= BLAS_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential LAPACK_LIBS=dc_lapack.a liblapack.a BLACS_LIBS=/opt/intel/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.a SCALAPACK_LIBS=-L/opt/intel/mkl/lib/intel64 -lmkl_scalapack_lp64 COMP_LIBS=dc_lapack.a liblapack.a libblas.a NETCDF_LIBS= NETCDF_INTERFACE= MPI_LIBS= -L/usr/lib/openmpi/lib -lmpi -lmpi_f90 -lmpi_f77 LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS) $(MPI_LIBS) -lpthread #SIESTA needs an F90 interface to MPI #This will give you SIESTA's own implementation #If your compiler vendor offers an alternative, you may change #to it here. MPI_INTERFACE=libmpi_f90.a MPI_INCLUDE=/usr/lib/openmpi/include #Dependency rules are created by autoconf according to whether #discrete preprocessing is necessary or not. .F.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $< .F90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $< .f.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $< .f90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<
Then build:
make

You can edit Tests/test.mk to make sure that it's pointing to your siesta executable (or make a symlink to siesta in /opt/siest/siesta-3.2-pl-5/) and that it uses mpirun and the appropriate number of threads.

Then run make in Tests/ to run all the tests.

05 June 2015

611. Building ecce on debian jessie

NOTE:
* I've confirmed that ECCE built like this installs and works perfectly on a Thinkpad SL410 with intel graphics

* It also compiles and runs perfectly on a home built desktop with external nvidia card (GF119) using the binary non-free nvidia drivers

* It also compiles and runs perfectly on a home built desktop with onboard nvidia (GeForce 7025/nForce 630a) using the nouveau drivers. I had issues on this desktop before, but reinstalled debian jessie from scratch. Before that I used nvidia-legacy drivers, which may or may not  (probably not) have had something to do with it not working.

* UPDATE: instead of putting
#include <freetype.h>
the recommended method is to use
#include FT_FREETYPE_H
I've updated the patch_script.sh below accordingly. Same goes for ftoutln.h vs FT_OUTLINE_H, but the latter didn't work (error saying #include must use "" or <>)

* UPDATE: If you're having issues with undetected -lGL and -lGLU in the wxwidgets step, it's because
667       endif
668       cat configure.orig | sed -e 's%^SEARCH_INCLUDE="\\%SEARCH_INCLUDE="$ECCE_HOME/${ECCE_SYSDIR}3rdparty/mesa/include \\%' >! configure
669       chmod a+x configure
670 

needs to be changed to
667       endif
668       cat configure.orig | sed -e 's%^SEARCH_INCLUDE="\\%SEARCH_INCLUDE="$ECCE_HOME/${ECCE_SYSDIR}3rdparty/mesa/include $ECCE_HOME/${ECCE_SYSDIR}3rdparty/mesa/lib \\%' >! configure
669       chmod a+x configure
670 
I had this issue on a debian wheezy system with the vendor nvidia libraries.
I wouldn't have spotted this bug otherwise.

* Another error from my debian wheezy nvidia system: if you get
checking how to run the C preprocessor... x86_64-linux-gnu-gcc -E ./configure: line 2880: syntax error near unexpected token `Using' ./configure: line 2880: `  AC_MSG_NOTICE(Using external PCRE library from $PCRE_CONFIG)'
then make sure you're not using autoconf2.13, which is an obsolete version. I think I have it due to my system originally being installed back in 2010.

* Finally, I'm currently  working on fixing minor things that have been nagging me in ecce. One is the basis set quicklist (in src/dsm/edsiimpl/ICalcUtils.C), but obviously that's a personal preference. A more serious one is the 256 character limit for csh commands:
Exceeds maximum C shell command length of 256 characters
Note that this isn't the C shell complaining -- this is a built-in limit in ecce (in src/comm/rcommand/RCommand.C). I've changed that limit to 16384 characters (the real limit is much, much higher)
I've also added two basis sets to ECCE, and have tinkered with the exchange-correlation functionals.

I'll try to push the fixes back upstreams when I'm ready if they'll accept them; otherwise I'll create my own github/sourceforge repo.

THE POST:
Building ECCE on debian wheezy was a breeze. Building ECCE on debian jessie was painful.

In the end it boiled down to two things:
*freetype headers are no longer in freetype2/freetype/ but in freetype2/

*-Wformat-security is turned on by default

mkdir ~/tmp/ecce_compile -p
cd ~/tmp/ecce_compile
sudo apt-get install bzip2 build-essential autoconf libtool ant pkg-config
sudo apt-get install gtk+-2.0-dev libxt-dev csh gfortran openjdk-7-jdk python-dev
sudo apt-get install libjpeg-dev imagemagick xterm libfreetype6-dev libfl-dev libtool-bin

As usual I'm not 100% sure when it comes to the necessary packages. libfl-dev might not be needed.

Download the ECCE source code and put the ecce-v7.0-src.tar.bz2 file in ~/tmp/ecce_compile. Put the patch_script.sh file (see below in this post for the code) in ~/tmp/ecce_compile. Then do
 
tar xvf ecce-v7.0-src.tar.bz2 
cd ecce-v7.0/
export ECCE_HOME=`pwd`
cd build/
./build_ecce

You'll now step through a list over programs and libraries that are needed and what ECCE can find. If you're having issues with e.g. javac and java being different versions, use sudo update-alternative --config javac.

At the end you'll be asked whether to skip these checks next time -- answer y(es).

Next do
./build_ecce|tee xerxes.log && ./build_ecce |tee mesa.log && ./build_ecce |tee wxwidgets.log
sh ../../patch_script.sh && ./build_ecce|tee wxpython.log 
./build_ecce|tee httpd.log && ./build_ecce|tee ecce.log

If all went well you've managed to build the ecce binaries. If not, go through wxpython.log and check for errors relating to format-security statements. Then go through ecce.log and look for issues with freetype.

What to do with the binaries? Follow one of the many ECCE installation posts on this blog, e.g. http://verahill.blogspot.com.au/2013/08/487-version-70-of-ecce-out-now.html

NOTE that if you get ''Invalid null command." trying to execute install_ecce.v7.0.csh, install tcsh and do
tcsh install_ecce.v7.0.csh

The patch_script.sh file -- when copying, make sure to check that the lines end where they are supposed to and not broken up.
#!/bin/bash cp ${ECCE_HOME}/build/3rdparty-dists/wxPython-src-2.8.12.1.tar.bz2 ${ECCE_HOME}/3rdparty/build/ cd ${ECCE_HOME}/3rdparty/build/ tar xvf wxPython-src-2.8.12.1.tar.bz2 rm wxPython-src-2.8.12.1.tar.bz2 cd ${ECCE_HOME}/3rdparty/build/wxPython-src-2.8.12.1/wxPython grep -rsl "PyErr_Format(PyExc_RuntimeError, mesg)" *|xargs -I {} sed -i 's/PyErr_Format(PyExc_RuntimeError, mesg)/PyErr_Format(PyExc_RuntimeError, "%s", mesg)/g' {} cd ${ECCE_HOME}/3rdparty/build/wxPython-src-2.8.12.1/wxPython/src/gtk/ sed -i 's/wxLogFatalError(m)/wxLogFatalError("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogError(m)/wxLogError("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogWarning(m)/wxLogWarning("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogMessage(m)/wxLogMessage("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogInfo(m)/wxLogInfo("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogDebug(m)/wxLogDebug("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogVerbose(m)/wxLogVerbose("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogStatus(pFrame, m)/wxLogStatus(pFrame, "%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogStatus(m)/wxLogStatus("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogSysError(m)/wxLogSysError("%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogGeneric(level, m)/wxLogGeneric(level, "%s", m.c_str())/g' _misc_wrap.cpp sed -i 's/wxLogTrace(mask, m)/wxLogTrace(mask, "%s", m.c_str())/g' _misc_wrap.cpp cd ${ECCE_HOME}/src grep -srl "<freetype/freetype.h>" |xargs -I {} sed -i 's,<freetype/freetype.h>,FT_FREETYPE_H,g' {} grep -srl "freetype/" |xargs -I {} sed -i 's,freetype/,,g' {} cd ${ECCE_HOME}/build


What I found during troubleshooting:

In files such as:
./3rdparty/build/wxPython-src-2.8.12.1/wxPython/src/gtk/_core_wrap.cpp
./3rdparty/build/wxPython-src-2.8.12.1/wxPython/src/gtk/_gdi_wrap.cpp
./3rdparty/build/wxPython-src-2.8.12.1/wxPython/src/gtk/_windows_wrap.cpp
./3rdparty/build/wxPython-src-2.8.12.1/wxPython/src/gtk/_controls_wrap.cpp
there are sections which look like this:
863 } else { 864 PyErr_Format(PyExc_RuntimeError, mesg); 865 }
Compiling with -Wformat-security means that you'll have to patch all those expression to
863 } else { 864 PyErr_Format(PyExc_RuntimeError, "%s", mesg); 865 }
There were similar issue with wxLog*(m) statements in other files, e.g.
3rdparty/build/wxPython-src-2.8.12.1/wxPython/src/gtk/_misc_wrap.cpp -> ("%s", m.c_str()) 3093 m.Replace(wxT("%"), wxT("%%")); 3094 wxLogFatalError(m); 3095 } .. 3177 m.Replace(wxT("%"), wxT("%%")); 3178 wxLogTrace(mask, m); 3179 }

29 May 2015

608. Bruker Topspin on Debian Jessie

Here's a more extensive description of how to install Bruker Topspin (student version):

Very briefly:
$ wget http://bruker.telemaxx.net/student/linux-topspin.sh
$ sudo dpkg --add-architecture i386
$ sudo apt-get update
$ sudo apt-get install libxft2:i386 libxtst6:i386 perl-tk libcups2:i386 openjdk-7-jdk
$ su -
# xauth merge /home/user/.Xauthority 
# exit
$ sh linux-topspin.sh
$ ~/carbon/topspin$ sh linux-topspin.sh 
Verifying archive integrity... All good.
Uncompressing TopSpin 3.2..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
NOTE: no display found - trying localhost:11.0
Using TCL_LIBRARY=/tmp/selfgz29293/linux/tcl-8.5.11/lib/tcl8.5
Using TK_LIBRARY=/tmp/selfgz29293/linux/tk-8.5.11/lib/tk8.5
Please enter root password if prompted for it.
Password: 
Starting /tmp/selfgz29293/linux/tk-8.5.11/bin/wish8.5 -f /tmp/selfgz29293/xwinstall.d/swim/lib/xwinstall.tcl --
Using log file: /tmp/install.log
Error while displaying /tmp/selfgz29293/rellet.pdf with /tmp/swim-29462/prog/bin/xpdf : 
/tmp/swim-29462/prog/bin/xpdf: error while loading shared libraries: libSM.so.6: cannot open shared object file: No such file or directory

Using log file: /opt/topspin3.2/install.log
Error: Cannot create user account flexlm: useradd flexlm: useradd: group flexlm exists - if you want to add this user to that group, use -g.
Errors occurred during installation:
Error: Cannot create user account flexlm: useradd flexlm: useradd: group flexlm exists - if you want to add this user to that group, use -g.
[I was doing this while logged in via ssh -XC to the student's computer, and without a pdf reader installed. If a pdf opens, close it to continue the installation. Don't worry about the errors.]

Here are screenshots from the installation process:
























The only thing that remained was to install the license.dat file that Bruker had issued to my student:

sudo mv /usr/local/flexlm/Bruker/licenses/license.dat /usr/local/flexlm/Bruker/licenses/license.bak sudo cp ~/carbon/topspin/license.dat /usr/local/flexlm/Bruker/licenses/license.dat
And then we were able to start topspin:







 And finally:

26 May 2015

607. Ping...Topspin and ADF work on debian jessie

My blog post productivity has been getting increasingly poor over the past year and a half, with a precipitous dip occurring at the beginning of this year. The dip is due to teaching and research, and the slow but steady decline preceding it is due to parenthood (the older the little one gets, the less time -- and inclination! -- I have to do extra work. Toddlers can be so much fun.).

I've got a few posts that need a bit of polishing before I publish ('how to set up your own DNS server' and 'how to set up your own mail server' are two examples), but until then, I'll seed your google search results with the following information about something completely different:

* Bruker Topspin 3.2 (https://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/overview.html) -- the NMR program, not the table tennis game -- installs fine on Debian Jessie 64 bit (the only version we tried). Note that:
** you'll need java
** you'll need the 32 bit package with libXtst.so.6, not the 64 bit package. It can be installed via apt-get install libxtst6:i386
** you'll need to enable the root account if you haven't already (the easiest way to do that is to do sudo passwd root, set a password and you're good to go)

* The trial version of the Amsterdam Density Functional package (ADF; http://www.scm.com/Downloads/2014) installs and runs fine* on one of my Debian Jessie 64 bit nodes. I did not install the intel mpi libraries, but then adf seems to be working according to a shared memory model.

Installation was quick and painless. I downloaded the package using the instructions in the email, copied the .tgz file to my node, ssh:d with X enabled (ssh -XC) to allow for interactive activation/registration, and to be able to use adfjobs (to draw molecules and set up jobs), and to be able to use adfview.

I untared the adf file:
tar xvf adf2014.07.pc64_linux.intelmpi.tgz

I then moved the folder to /opt and took ownership of it:
sudo mv adf2014.07 /opt/
sudo chown $USER:$USER /opt/adf2014.07 -R

I edited /opt/adf2014.07/adfrc.sh to read:
ADFHOME=/opt/adf2014.07

And then sourced it and ran adfjobs:
source adfrc.sh
bin/adfjobs

I was then asked to provide the username and password from my email, and from that point on it was just a matter of using the program (which has it's own quirks ).

*by default only six cores on a hex core i7-4930k are used. To force 12 cores (hyperthreading) you need to explicitly tell ADF to do so. The manual says not to, however. I haven't done any performance tests, BUT without specifying 12 cores the node is only running at half load.

02 November 2014

600. gdm/gnome breakage in debian jessie October/November 2014

I did a dist-upgrade last night and encountered this on my next boot:
During the dist-upgrade I got a message about the nvidia driver version not being compatible with my system -- small surprise as I have an onboard intel chip and no external graphics card (it's a lenovo thinkpad SL410).

Installing kdm let me at least boot into a DM. I still couldn't launch gnome from kdm, it giving the same error message as in the photo.
Digging a bit deeper and looking at what happened before/during a crash:
journalctl
Nov 02 10:46:30 niobium kdm[1317]: Stopping K Display Manager: kdm...done. Nov 02 10:46:30 niobium systemd[1]: gdm.service: control process exited, code=exited status=1 Nov 02 10:46:30 niobium systemd[1]: Failed to start GNOME Display Manager. Nov 02 10:46:30 niobium systemd[1]: Dependency failed for X11 Display Manager. Nov 02 10:46:30 niobium systemd[1]: Unit gdm.service entered failed state. Nov 02 10:46:30 niobium kdm[1350]: Starting K Display Manager: kdm. Nov 02 10:46:30 niobium sudo[1311]: pam_unix(sudo:session): session closed for user root Nov 02 10:46:30 niobium console-kit-daemon[1707]: (process:1372): GLib-CRITICAL **: g_slice_set_config: assertion 'sys_page_size == 0' failed Nov 02 10:46:30 niobium console-kit-daemon[1707]: (process:1373): GLib-CRITICAL **: g_slice_set_config: assertion 'sys_page_size == 0' failed Nov 02 10:46:30 niobium console-kit-daemon[1707]: (process:1374): GLib-CRITICAL **: g_slice_set_config: assertion 'sys_page_size == 0' failed Nov 02 10:46:30 niobium kdm_greet[1378]: Cannot load /usr/share/kde4/apps/kdm/faces/.default.face: No such file or directory Nov 02 10:46:31 niobium systemd[1]: gdm.service: control process exited, code=exited status=1 Nov 02 10:46:31 niobium systemd[1]: Failed to start GNOME Display Manager. Nov 02 10:46:31 niobium systemd[1]: Dependency failed for X11 Display Manager. Nov 02 10:46:31 niobium systemd[1]: Unit gdm.service entered failed state. Nov 02 10:46:32 niobium console-kit-daemon[1707]: (process:1398): GLib-CRITICAL **: g_slice_set_config: assertion 'sys_page_size == 0' failed Nov 02 10:46:32 niobium console-kit-daemon[1707]: (process:1399): GLib-CRITICAL **: g_slice_set_config: assertion 'sys_page_size == 0' failed Nov 02 10:46:32 niobium console-kit-daemon[1707]: (process:1400): GLib-CRITICAL **: g_slice_set_config: assertion 'sys_page_size == 0' failed Nov 02 10:46:32 niobium systemd[1]: gdm.service: control process exited, code=exited status=1 Nov 02 10:46:32 niobium systemd[1]: Failed to start GNOME Display Manager. Nov 02 10:46:32 niobium systemd[1]: Dependency failed for X11 Display Manager. Nov 02 10:46:32 niobium systemd[1]: Unit gdm.service entered failed state. Nov 02 10:46:33 niobium systemd[1]: gdm.service: control process exited, code=exited status=1 Nov 02 10:46:33 niobium systemd[1]: Failed to start GNOME Display Manager. Nov 02 10:46:33 niobium systemd[1]: Dependency failed for X11 Display Manager. Nov 02 10:46:33 niobium systemd[1]: Unit gdm.service entered failed state. Nov 02 10:46:35 niobium systemd[1]: gdm.service start request repeated too quickly, refusing to start. Nov 02 10:46:35 niobium systemd[1]: Failed to start GNOME Display Manager. Nov 02 10:46:35 niobium systemd[1]: Dependency failed for X11 Display Manager. Nov 02 10:46:35 niobium systemd[1]: Unit gdm.service entered failed sta
GDM shouldn't be involved at all as I was using kdm.
systemctl -l status gdm.service
● gdm.service - GNOME Display Manager Loaded: loaded (/lib/systemd/system/gdm.service; enabled) Drop-In: /run/systemd/generator/gdm3.service.d └─50-gdm3-$x-display-manager.conf Active: failed (Result: start-limit) since Sun 2014-11-02 10:46:35 AEDT; 14min ago Process: 1405 ExecStartPre=/bin/sh -c [ "$(cat /etc/X11/default-display-manager 2>/dev/null)" = "/usr/sbin/gdm3" ] (code=exited, status=1/FAILURE) Nov 02 10:46:35 niobium systemd[1]: gdm.service start request repeated too quickly, refusing to start. Nov 02 10:46:35 niobium systemd[1]: Failed to start GNOME Display Manager. Nov 02 10:46:35 niobium systemd[1]: Unit gdm.service entered failed state.


The solution:
Either way, I now had enough keywords to start googling, and came across http://forums.debian.net/viewtopic.php?f=10&t=118305

Basically,
sudo apt-get purge nvidia-*
sudo apt-get purge libnvidia-ml1:i386 nvidia-smi:i386
sudo apt-get install glx-alternative-mesa
sudo apt-get --reinstall install gdm3

Launching gnome (standard) from kdm gave me prompts to set up the configuration for an installed extension (I miss the frippery extensions...). Not sure whether the breakage was related to the extension.
 Either way, everything is working properly now.

28 July 2014

586.Very Briefly: Gnuradio, RTL-SDR, GQRX and an R280T device on debian jessie

NOTE:
* I did this on debian jessie which at the time has gnuradio v 3.7.3-9+b1 and rtl-sdr v 0.5.3-3

* I'm having a lot of trouble getting gqrx working on debian wheezy even with backports. Whereas the backports versions of gnuradio, rtl-sdr and gqrx-sdr install just fine, when running gqrx I get the following error:
gqrx: symbol lookup error: /usr/lib/x86_64-linux-gnu/libQtNetwork.so.4: undefined symbol: _ZN16QIODevicePrivate13putCharHelperEc
* gqrx won't work on debian wheezy systems with 2 Gb of memory for some reason. I get the same error as is shown in this post: https://groups.google.com/forum/#!topic/gqrx/20F8RMWkNbU

The post:
I recently bought a DVB USB dongle based on RTL2832 and R280T: http://www.ebay.com.au/itm/221450623699?ssPageName=STRK:MEWNX:IT&_trksid=p3984.m1497.l2649. AU$11for a TV card which actually works flawlessly under linux really isn't bad!

As I already have a mythtv setup using leadtek DTV 1000S I was more interested in exploring the R820T dongle as a software defined radio (SDR).

 So, after glancing at  http://www.thepowerbase.com/2012/06/getting-started-with-rtl-sdr/2/ I did the following


sudo apt-get install rtl-sdr gnuradio gnuradio-dev libgnuradio-osmosdr0.1.1.4 git libboost-dev liblog4cpp5-dev libboost-system-dev libboost-program-options-dev checkinstall
mkdir ~/tmp
cd ~/tmp
git clone https://github.com/csete/gqrx.git gqrx.git
cd gqrx.git/
mkdir build
cd build
qmake ../
make
sudo checkinstall --install=no
0 - Maintainer: [ root@niobium ] 1 - Summary: [ gqrx ] 2 - Name: [ gqrx ] 3 - Version: [ 20140726 ] 4 - Release: [ 1 ] 5 - License: [ GPL ] 6 - Group: [ checkinstall ] 7 - Architecture: [ amd64 ] 8 - Source location: [ build ] 9 - Alternate source location: [ ] 10 - Requires: [ ] 11 - Provides: [ build ] 12 - Conflicts: [ ] 13 - Replaces: [ ]
sudo dpkg -i gqrx_20140726-1_amd64.deb

Starting gqrx and using it is easy:
gqrx
So far I haven't managed to get anything other than regular commercial radio signals (I've only explored the FM band).

27 December 2013

539. Laptop not suspending on closing lid in Debian Jessie/Gnome 3.8.4 -- need to use systemd

Edit: I suspect that there are solutions out there that don't require systemd. It just happened that this was the path of least resistance, at least for my laptop which has a fairly simple set up. Not sure my work cluster would be so straight-forward...

Original post:
Closing the laptop lid doesn't have any effect. dmesg returns
[95643.717984] systemd-logind[2731]: Lid closed.
[95643.718173] systemd-logind[2731]: Suspending...
[95648.722146] systemd-logind[2731]: Delay lock is active but inhibitor timeout is reached.
[95648.735369] systemd-logind[2731]: Failed to send delayed message: Launch helper exited with unknown return code 1
(also, why are we suddenly requiring systemd? I thought debian was going to be free from that...that...abomination...but I suppose this will be fixed before jessie goes stable in a couple of years)

Anyway, the issue seems to be that systemd hasn't got PID 1:
Working suspend/resume requires systemd to be PID 1 [1]. Boot with init=/bin/systemd for that.
And in my case I had
init=/sbin/bootchartd
in my GRUB_CMDLINE_LINUX_DEFAULT which I changed to
init=/bin/bootchartd
. Note that my full line is
GRUB_CMDLINE_LINUX_DEFAULT="quiet drm_kms_helper.poll=N init=/bin/systemd initcall_debug printk.time=y resume=UUID=8adf424c-c375-4035-8d5d-181489b4461b resume_offset=7182336"
where the resume commands are related to this post about hibernation using a swap file, and the drm_kms_helper.poll is related to this issue.

Anyway, rebooting gives
ps aux|grep systemd
root         1  0.1  0.1  46104  4668 ?        Ss   07:31   0:00 /bin/systemd
root       202  0.0  0.4 144868 18416 ?        Ss   07:31   0:00 /lib/systemd/systemd-journald
root       221  0.0  0.0  38500  2292 ?        Ss   07:31   0:00 /lib/systemd/systemd-udevd
root       877  0.0  0.0  37024  1760 ?        Ss   07:31   0:00 /lib/systemd/systemd-logind
message+   887  0.1  0.0  29148  2520 ?        Ss   07:31   0:00 /usr/bin/dbus-daemon --system --address=systemd: --nofork --nopidfile --systemd-activation

Closing (and opening) the lid gives

dmesg|grep PM
[..]
[  444.637761] PM: Syncing filesystems ... done.
[  444.668607] PM: Preparing system for mem sleep
[  444.784170] PM: Entering mem sleep
[  445.232203] PM: suspend of devices complete after 447.606 msecs
[  445.232862] PM: late suspend of devices complete after 0.650 msecs
[  445.277535] PM: noirq suspend of devices complete after 44.667 msecs
[  445.360219] PM: Saving platform NVS memory
[..]
[  445.509662] PM: noirq resume of devices complete after 100.525 msecs
[  445.510133] PM: early resume of devices complete after 0.295 msecs
[  447.065176] PM: resume of devices complete after 1555.037 msecs
[  447.151847] PM: Finishing wakeup.

i.e. it works.

So I'm now using systemd, I suppose. However, I have yet to explore whether I can still use my precious /etc/network/interfaces file. At least my network interfaces haven't been renamed using the systemd nomeclature which annoyed me so much back when I used Arch, and my /etc/udev/rules.d/70-persistent-net.rules are still respected.

25 December 2013

538. Briefly: Sort folders before files in nautilus 3.8

I'm running debian jessie (current testing) on my laptop and after having held off upgrading for a while since I had to take it to a conference and didn't want to risk ending up with a broken system, I finally took the leap. I notice that there are a lot of references to systemd in dmesg, but haven't had a look at what it actually means -- are we past init and fully switched to systemd now? Or how do I go about modifying my network configuration if I can't use /etc/network/interfaces?

Anyway, one annoying little thing is that in Nautilus the folder content by default is arranged in alphabetical order, regardless of whether it's a file or a directory. The old behaviour was to arrange folders in alphabetical order, then files.

Here's how to get it back to 'normal' behaviour:
 
The new behaviour
Click on the 'Files' menu on the top desktop bar, select preferences:
Check 'Sort folders before files' to get back the normal behaviour
Check sort folders before files to make Nautilus behave well again

08 May 2013

407. Building less (458) as a temporary solution on Debian Jessie

Currently less conflicts with man-db/yelp/gnome-core/gnome on debian jessie. There are probably ways of overriding the conflict, but I prefer to simply compile my own less and install it.

Note that this doesn't take into account WHY less and man-db are listed as conflicting for versions of less below 4.5.6. I simply want less and the way to do it is to compile an approved version of less.

sudo apt-get install build-essential checkinstall
wget http://www.greenwoodsoftware.com/less/less-458.tar.gz
tar xvf less-458.tar.gz
cd less-458/
./configure
make
sudo checkinstall
0 - Maintainer: [ root@niobium ] 1 - Summary: [ less 4.5.8 ] 2 - Name: [ less ] 3 - Version: [ 458 ] 4 - Release: [ 1 ] 5 - License: [ GPL ] 6 - Group: [ checkinstall ] 7 - Architecture: [ amd64 ] 8 - Source location: [ less-458 ] 9 - Alternate source location: [ ] 10 - Requires: [ ] 11 - Provides: [ less ] 12 - Conflicts: [ ] 13 - Replaces: [ ]

07 May 2013

405. First breakage in Debian Jessie? less vs man-db

Update 12/5/13: less 456 is in the debian repos now so the breakage is resolved:
http://packages.debian.org/search?keywords=less

For some reason less (<456) and man-db conflict. man-db in turn is a requirement for yelp, which is a requirement for gnome-core which is a requirement for gnome. In other words, you currently have a choice between less or gnome.

More here: http://www.mail-archive.com/debian-bugs-dist@lists.debian.org/msg1117622.html

verahill@debianstd:~/tmp/poppler_build$ sudo apt-get install less
Reading package lists... Done Building dependency tree Reading state information... Done The following packages will be REMOVED: gnome gnome-core gnome-user-guide man-db yelp The following NEW packages will be installed: less 0 upgraded, 1 newly installed, 5 to remove and 0 not upgraded. Need to get 0 B/135 kB of archives. After this operation, 29.4 MB disk space will be freed. Do you want to continue [Y/n]?