Getting sado on peregrine

[Lumphie]

# C++14
QMAKE_CXX = g++-
QMAKE_LINK = g++-
QMAKE_CC = gcc-
QMAKE_CXXFLAGS += -std=c++14
# -Weffc++ goes bad with Qt
QMAKE_CXXFLAGS += -Wall -Wextra -Wshadow -Wnon-virtual-dtor -pedantic

# Debug and release mode
CONFIG += debug_and_release

# In release mode, turn on profiling
CONFIG(release, debug|release) {

  DEFINES += NDEBUG

  # gprof
  QMAKE_CXXFLAGS += -pg
  QMAKE_LFLAGS += -pg

}

# In debug mode, turn on gcov and UBSAN
CONFIG(debug, debug|release) {

  # gcov
  QMAKE_CXXFLAGS += -fprofile-arcs -ftest-coverage
  LIBS += -lgcov

  # UBSAN
  QMAKE_CXXFLAGS += -fsanitize=undefined
  QMAKE_LFLAGS += -fsanitize=undefined
  LIBS += -lubsan

  # Only in debug mode, a warning is an error
  QMAKE_CXXFLAGS += -Werror
}

# Qt needed for hiostogram to png
QT += core gui widgets

# Fixes
#/usr/include/boost/math/constants/constants.hpp:277: error: unable to find numeric literal operator 'operator""Q'
#   BOOST_DEFINE_MATH_CONSTANT(half, 5.000000000000000000000000000000000000e-01, "5.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000e-01")
#   ^
QMAKE_CXXFLAGS += -fext-numeric-literals

# Prevent Qt for failing with this error:
# qrc_[*].cpp:400:44: error: ‘qInitResources_[*]__init_variable__’ defined but not used
# [*]: the resource filename
QMAKE_CXXFLAGS += -Wno-unused-variable

include(sado.pri)
#include(kewe.pri)
include(pbd.pri)
include(histogram_to_png.pri)
include(../gausser/gausser.pri)
include(gsl.pri)

# Boost.Graph
LIBS += -lboost_graph
include(../BoostGraphTutorial/BoostGraphTutorial/boost_graph_tutorial.pri)

include(../SurfacePlotter/QtSurfacePlotWidget.pri)

SOURCES += sado_main.cpp

I can't make this.

It get errors like these:

error: no type named ‘type’ in ‘struct boost::container_gen<boost::listS, boost::list_edge<long unsigned int, boost::property<boost::edge_bundle_t, int, boost::no_property> > >’
           DirectedEdgeIter, UndirectedEdgeIter>::type edge_iterator;

[Lumphie]

I ran

module load Qt module load GCC/5.1.0

[Lumphie]

@richelbilderbeek any ideas?

[richelbilderbeek]

module load boost

or

module load Boost

[Lumphie]

loading Boost did it. But now I somehow don't have the permission to run it.

/usr/bin/xvfb-run: line 181: ./sado_peregrine: Permission denied

[richelbilderbeek]

Perhaps:

chmod +x sado_peregrine
./sado_peregrine

or

sudo ./sado_peregrine

(but that latter option is scary)

[richelbilderbeek]

Ah, I checked the xvfb wikipedia page. xvfb is for displaying graphics. Either (1) start ssh allowing for X:

ssh -X s123456@peregrine.hpc.rug.nl

or (2) remove the displayal of graphic things.

[Lumphie]

Peregrine is broken now. I think I did all of the above, but can't test it now.

[Lumphie]

Peregrine will probably be fixed tomorrow!

[Lumphie]

@richelbilderbeek

Lots of these.

In file included from /software/software/Boost/1.61.0-foss-2016a/include/boost/graph/adjacency_list.hpp:246:0,
                 from sado_int_edge.h:4,
                 from sado_int_edge.cpp:1:
/software/software/Boost/1.61.0-foss-2016a/include/boost/graph/detail/adjacency_list.hpp: In functie ‘sado::indiv_edg_desc sado::add_int_edge(const vert_desc&, const vert_desc&, int, sado::pedigree_graph&)’:
/software/software/Boost/1.61.0-foss-2016a/include/boost/graph/detail/adjacency_list.hpp:2235:43: let op: ‘p’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       typename Config::edge_property_type p;

And in the end this one.

collect2: fout: ld gaf exit-status 1 terug
make[1]: *** [sado_peregrine] Fout 1
make[1]: Map '/home/s2260050/pbdmms' wordt verlaten
make: *** [release] Fout 2

[richelbilderbeek]

Thanks. I will hopefully look at this soon.

Workaround: just remove -Werror in the .pro files for Peregrine builds.

[Lumphie]

In file included from /software/software/Boost/1.61.0-foss-2016a/include/boost/graph/adjacency_list.hpp:246:0,
                 from sado_indiv_graph.h:4,
                 from sado_indiv_graph.cpp:1:
/software/software/Boost/1.61.0-foss-2016a/include/boost/graph/detail/adjacency_list.hpp: In constructor ‘boost::adj_list_edge_property_map<Directed, Value, Ref, Vertex, Property, Tag>::adj_list_edge_property_map(Tag)’:
/software/software/Boost/1.61.0-foss-2016a/include/boost/graph/detail/adjacency_list.hpp:2653:59: let op: declaration of ‘tag’ shadows a member of ‘boost::adj_list_edge_property_map<Directed, Value, Ref, Vertex, Property, Tag>’ [-Wshadow]
       explicit adj_list_edge_property_map(Tag tag = Tag()): tag(tag) {}
                                                           ^
/software/software/Boost/1.61.0-foss-2016a/include/boost/graph/detail/adjacency_list.hpp:2652:11: note: shadowed declaration is here
       Tag tag;
           ^

This one is from today.

[richelbilderbeek]

Blimey, Boost.Graph shadows parameters! I may look closer into that one.

Worksaround: remove -Wshadow in the .pro file.

[Lumphie]

I removed all error checking in the .pro file and saved it under a different name, but somehow it magically still shows the errors.

[richelbilderbeek]

Can you show one?

[Lumphie]

# C++14
QMAKE_CXX = g++
QMAKE_LINK = g++
QMAKE_CC = gcc
QMAKE_CXXFLAGS += -std=c++1y

# Debug and release mode
CONFIG += debug_and_release

# Qt needed for hiostogram to png
QT += core gui widgets

# Fixes
#/usr/include/boost/math/constants/constants.hpp:277: error: unable to find numeric literal operator 'operator""Q'
#   BOOST_DEFINE_MATH_CONSTANT(half, 5.000000000000000000000000000000000000e-01, "5.00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000e-01")
#   ^
QMAKE_CXXFLAGS += -fext-numeric-literals

# Prevent Qt for failing with this error:
# qrc_[*].cpp:400:44: error: ‘qInitResources_[*]__init_variable__’ defined but not used
# [*]: the resource filename
QMAKE_CXXFLAGS += -Wno-unused-variable

include(sado.pri)
#include(kewe.pri)
include(pbd.pri)
include(histogram_to_png.pri)
include(../gausser/gausser.pri)
include(gsl.pri)

#Boost.Graph
LIBS += -lboost_graph
include(../BoostGraphTutorial/BoostGraphTutorial/boost_graph_tutorial_helper.pri)
include(../BoostGraphTutorial/BoostGraphTutorial/boost_graph_tutorial_no_properties.pri)

include(../SurfacePlotter/QtSurfacePlotWidget.pri)

SOURCES += sado_main.cpp
[s2260050@peregrine pbdmms]$ nano sado_peregrine1.pro

  GNU nano 2.0.9         Bestand: sado_peregrine1.pro                           

include(../gausser/gausser.pri)
include(gsl.pri)

#Boost.Graph
LIBS += -lboost_graph
include(../BoostGraphTutorial/BoostGraphTutorial/boost_graph_tutorial_helper.pr$
include(../BoostGraphTutorial/BoostGraphTutorial/boost_graph_tutorial_no_proper$

include(../SurfacePlotter/QtSurfacePlotWidget.pri)

SOURCES += sado_main.cpp

[richelbilderbeek]

Ah, replace

# C++14
QMAKE_CXX = g++
QMAKE_LINK = g++
QMAKE_CC = gcc
QMAKE_CXXFLAGS += -std=c++1y

by

# C++14
CONFIG += c++14
QMAKE_CXXFLAGS += -std=c++14

or if the first does not work

# C++14
CONFIG += c++14
QMAKE_CXXFLAGS += -std=c++1y

Ah, and remove these lines altogether, if those were in the script:

[s2260050@peregrine pbdmms]$ nano sado_peregrine1.pro

  GNU nano 2.0.9         Bestand: sado_peregrine1.pro    

[Lumphie]

Oh those last ones are not actually in there, but that's just a copy error from my terminal.

[Lumphie]

Still getting the same errors though.

[richelbilderbeek]

Also, maybe add to sado_peregrine1.pro the line:

include(sado.pri)

Would that work?

[Lumphie]

I'll try that. Also K3 is on the radio downstairs!

[richelbilderbeek]

I come down now!

[Lumphie]

Still the same error.

[Lumphie]

more undefined references to `boost::detail::graph::read_graphviz_new(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, boost::detail::graph::mutate_graph*)' follow
collect2: fout: ld gaf exit-status 1 terug

[richelbilderbeek]

Shucks. I am working on it :muscle:

[richelbilderbeek]

Note to self: it compiles and links fine on my LWP, using build_sado_peregrine that uses sado_peregrine.pro

[richelbilderbeek]

Note to self: hypothesis: Boost version mismatches Graphviz its version

[richelbilderbeek]

Note to self: reproduced the error on Peregrine :wrench:

[richelbilderbeek]

Note to self:

module load Graphviz; module load GCC/5.1.0; module load Boost; make

to investigate closer

[richelbilderbeek]

It works.

Just run ./sado_peregrine_build

If it does not show the Golden Standard, let me know.

You can use that script to base the rest on.

I will start profiling again :+1:

[Lumphie]

[s2260050@peregrine simulations]$ squeue -u $USER JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 11069126 nodes kewe_sad s2260050 R 0:15 1 pg-node089

[Lumphie]

We're up and running!

[Lumphie]

100 GB 8 days should be enough.

[Lumphie]

Got 2 jobs going.

1. 4000 generations around 250 individuals per generation
2. 4000 generations around 1500 (for now) individuals per generation

First simulation is done, but I'm waiting for the graphing of the tree. That's gonna take a long time. Second job is going to take even longer!

[richelbilderbeek]

Looking at #251 there are hints for some exponentials in the time :-(

[Lumphie]

Tip: type 'sudo apt-get install graphviz' in the command line
convert_dot_to_svg: 'dot' cannot be found. type 'sudo apt-get install graphviz' in the command line

Yeaahhh.. I don't think I'm allowed to do that.

[richelbilderbeek]

Yeaahhh.. I don't think I'm allowed to do that.

Depend on the computer :wiseguy: :hipster: :sunglasses:

[Lumphie]

It's on peregrine. On my peregrine account I'm not allowed to use sudo. (I'm on the "unauthorized sudo user"-list twice now. So not gonna risk it. Any way around it?

[richelbilderbeek]

module load Graphviz

[Lumphie]

Ik zag dat je al een mailtje had gestuurd.

ssh: connect to host peregrine.hpc.rug.nl port 22: Connection timed out

[Lumphie]

Runs fine now