Package Details: silo 4.10.2-5

Git Clone URL: https://aur.archlinux.org/silo.git (read-only)
Package Base: silo
Description: A Mesh and Field I/O Library and Scientific Database
Upstream URL: https://wci.llnl.gov/simulation/computer-codes/silo
Licenses: custom, BSD
Submitter: jedbrown
Maintainer: eolianoe
Last Packager: eolianoe
Votes: 5
Popularity: 0.006695
First Submitted: 2009-02-13 15:59
Last Updated: 2016-06-13 11:11

Latest Comments

eolianoe commented on 2016-08-24 09:09

@fallenrgh: building fine here for now, I will add the `-std=c++98` flags if there is more trouble

fallenrgh commented on 2016-08-23 21:14

Building this package fails for me using the gcc default -std=gnu++14. You get errors like the example from smradlev below.

/usr/include/c++/6.1.1/tuple:121:28: error: expected ‘)’ before ‘,’ token
_Head_base(allocator_arg_t, __uses_alloc1<_Alloc> __a)

Switching to -std=c++98 did the trick for me.

eolianoe commented on 2016-06-13 10:01

@smradlev: building fine here even in a clean chroot, could give me the full build log by mail? Also next time please do not paste full log in comments and edit your comments to make it easier to read.

EDIT: Your build failure seems to come from hdf5-openmpi, added a patch to get it works with it

smradlev commented on 2016-06-13 09:16

I'm getting the following error when trying to build the package. It seems it's trying to compile a sh script file with g++ for some reason.

libtool: link: g++ -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -o .libs/csg csg.o -L/usr/lib -L/usr/lib/lib ../src/.libs/libsiloh5.so -lhdf5 -lz -lm -lsz
g++ -DHAVE_CONFIG_H -I. -I.. -I./../src/silo -I./../src/silo -I/usr/include -I/usr/include -D_FORTIFY_SOURCE=2 -I/usr/include -rdynamic -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -MT rocket-rocket.o -MD -MP -MF .deps/rocket-rocket.Tpo -c -o rocket-rocket.o `test -f 'rocket.cxx' || echo './'`rocket.cxx
rocket.cxx:55:2: warning: #warning MAKE THIS CONDITIONAL LATER [-Wcpp]
#warning MAKE THIS CONDITIONAL LATER
^~~~~~~
In file included from /usr/include/c++/6.1.1/tuple:39:0,
from /usr/include/c++/6.1.1/bits/stl_map.h:63,
from /usr/include/c++/6.1.1/map:61,
from rocket.cxx:66:
./array:1:2: error: invalid preprocessing directive #!
#! /bin/sh
^
./array:3:3: error: invalid preprocessing directive #array
# array - temporary wrapper script for .libs/array
^~~~~
./array:4:3: error: invalid preprocessing directive #Generated
# Generated by ltmain.sh (GNU libtool) 2.2.6b
^~~~~~~~~
./array:6:3: error: invalid preprocessing directive #The
# The array program cannot be directly executed until all the libtool
^~~
./array:7:3: error: invalid preprocessing directive #libraries
# libraries that it depends on are installed.
^~~~~~~~~
./array:9:3: error: invalid preprocessing directive #This
# This wrapper script should never be moved out of the build directory.
^~~~
./array:10:3: error: invalid preprocessing directive #If
# If it is, it will not operate correctly.
^~
./array:12:3: error: invalid preprocessing directive #Sed
# Sed substitution that helps us do robust quoting. It backslashifies
^~~
./array:13:3: error: invalid preprocessing directive #metacharacters
# metacharacters that are still active within double-quoted strings.
^~~~~~~~~~~~~~
./array:17:3: error: invalid preprocessing directive #Be
# Be Bourne compatible
^~
./array:21:5: error: invalid preprocessing directive #Zsh
# Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
^~~
./array:22:5: error: invalid preprocessing directive #is
# is contrary to our usage. Disable this feature.
^~
./array:26:8: error: stray ‘`’ in program
case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
^
./array:26:29: error: stray ‘`’ in program
case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
^
./array:28:28: error: stray ‘#’ in program
BIN_SH=xpg4; export BIN_SH # for Tru64
^
./array:29:29: error: stray ‘#’ in program
DUALCASE=1; export DUALCASE # for MKS sh
^
./array:31:3: error: invalid preprocessing directive #The
# The HP-UX ksh and POSIX shell print the target directory to stdout
^~~
./array:32:13: error: missing binary operator before token "is"
# if CDPATH is set.
^~
./array:32:0: error: unterminated #if
# if CDPATH is set.

In file included from /usr/include/c++/6.1.1/tuple:39:0,
from /usr/include/c++/6.1.1/bits/stl_map.h:63,
from /usr/include/c++/6.1.1/map:61,
from rocket.cxx:66:
./array:14:1: error: ‘Xsed’ does not name a type
Xsed='/usr/bin/sed -e 1s/^X//'
^~~~
./array:18:66: error: ‘then’ does not name a type
if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
^~~~
./array:26:58: error: ‘esac’ does not name a type
case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
^~~~
./array:28:21: error: ‘BIN_SH’ does not name a type
BIN_SH=xpg4; export BIN_SH # for Tru64
^~~~~~
./array:29:20: error: ‘DUALCASE’ does not name a type
DUALCASE=1; export DUALCASE # for MKS sh
^~~~~~~~
In file included from /usr/include/c++/6.1.1/bits/stl_map.h:63:0,
from /usr/include/c++/6.1.1/map:61,
from rocket.cxx:66:
/usr/include/c++/6.1.1/tuple:71:33: error: expected ‘)’ before ‘,’ token
_Head_base(allocator_arg_t, __uses_alloc0)
^
/usr/include/c++/6.1.1/tuple:75:28: error: expected ‘)’ before ‘,’ token
_Head_base(allocator_arg_t, __uses_alloc1<_Alloc> __a)
^
/usr/include/c++/6.1.1/tuple:79:28: error: expected ‘)’ before ‘,’ token
_Head_base(allocator_arg_t, __uses_alloc2<_Alloc> __a)
^
/usr/include/c++/6.1.1/tuple:83:26: error: expected ‘)’ before ‘,’ token
_Head_base(__uses_alloc0, _UHead&& __uhead)
^
/usr/include/c++/6.1.1/tuple:87:26: error: expected ‘)’ before ‘<’ token
_Head_base(__uses_alloc1<_Alloc> __a, _UHead&& __uhead)
^
/usr/include/c++/6.1.1/tuple:91:26: error: expected ‘)’ before ‘<’ token
_Head_base(__uses_alloc2<_Alloc> __a, _UHead&& __uhead)
^
/usr/include/c++/6.1.1/tuple:117:33: error: expected ‘)’ before ‘,’ token
_Head_base(allocator_arg_t, __uses_alloc0)
^
/usr/include/c++/6.1.1/tuple:121:28: error: expected ‘)’ before ‘,’ token
_Head_base(allocator_arg_t, __uses_alloc1<_Alloc> __a)
^
/usr/include/c++/6.1.1/tuple:125:28: error: expected ‘)’ before ‘,’ token
_Head_base(allocator_arg_t, __uses_alloc2<_Alloc> __a)
^
/usr/include/c++/6.1.1/tuple:129:26: error: expected ‘)’ before ‘,’ token
_Head_base(__uses_alloc0, _UHead&& __uhead)
^
/usr/include/c++/6.1.1/tuple:133:26: error: expected ‘)’ before ‘<’ token
_Head_base(__uses_alloc1<_Alloc> __a, _UHead&& __uhead)
^
/usr/include/c++/6.1.1/tuple:138:26: error: expected ‘)’ before ‘<’ token
_Head_base(__uses_alloc2<_Alloc> __a, _UHead&& __uhead)
^
/usr/include/c++/6.1.1/tuple:237:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a)
^~~~~
/usr/include/c++/6.1.1/tuple:242:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:250:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:257:37: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:263:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:270:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:278:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:380:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a)
^~~~~
/usr/include/c++/6.1.1/tuple:384:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:389:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:395:37: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:400:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:406:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:412:30: error: expected ‘)’ before ‘__tag’
_Tuple_impl(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:711:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a)
^~~~~
/usr/include/c++/6.1.1/tuple:721:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:732:33: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:742:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:753:33: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:759:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a, const tuple& __in)
^~~~~
/usr/include/c++/6.1.1/tuple:763:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a, tuple&& __in)
^~~~~
/usr/include/c++/6.1.1/tuple:772:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:784:33: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:796:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:808:33: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1021:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a)
^~~~~
/usr/include/c++/6.1.1/tuple:1032:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1044:33: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1054:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a, _U1&& __a1, _U2&& __a2)
^~~~~
/usr/include/c++/6.1.1/tuple:1064:33: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1070:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a, const tuple& __in)
^~~~~
/usr/include/c++/6.1.1/tuple:1074:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a, tuple&& __in)
^~~~~
/usr/include/c++/6.1.1/tuple:1083:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1095:33: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1107:24: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a, tuple<_U1, _U2>&& __in)
^~~~~
/usr/include/c++/6.1.1/tuple:1117:33: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1128:31: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1138:40: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
/usr/include/c++/6.1.1/tuple:1148:31: error: expected ‘)’ before ‘__tag’
tuple(allocator_arg_t __tag, const _Alloc& __a, pair<_U1, _U2>&& __in)
^~~~~
/usr/include/c++/6.1.1/tuple:1158:40: error: expected ‘)’ before ‘__tag’
explicit tuple(allocator_arg_t __tag, const _Alloc& __a,
^~~~~
rocket.cxx:155:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
};
^
rocket.cxx:155:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
rocket.cxx:155:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
rocket.cxx:155:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
rocket.cxx:155:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
rocket.cxx: In function ‘int WriteAllFormats(int, char**)’:
rocket.cxx:744:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
char *dirs[] = {".", "../..", ".libs", "../../.libs"};
^
rocket.cxx:744:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
rocket.cxx:744:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
rocket.cxx:744:57: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
make[1]: *** [Makefile:1623: rocket-rocket.o] Error 1
make[1]: Leaving directory '/home/user/Build/silo/src/silo-4.10.2/tests'
make: *** [Makefile:1777: check-am] Error 2
==> ERROR: A failure occurred in check().
Aborting...

ftschindler commented on 2016-01-28 22:04

Building this package fails with the following error:
```
libtool: link: g++ -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fstack-check -Wl,-O1 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -o .libs/silock silock.o -L/usr/lib -L/usr/lib/lib ../../src/.libs/libsiloh5.so -lhdf5 -lz -lm -lsz
../../src/.libs/libsiloh5.so: undefined reference to `H5Pset_fapl_mpiposix'
collect2: error: ld returned 1 exit status
Makefile:403: recipe for target 'silock' failed
```
This is not surprising, see e.g.: http://hdf-forum.184993.n3.nabble.com/Re-undefined-reference-to-H5Pset-fapl-mpiposix-td4027216.html

Disabling the `hdf5` dependency seems to work for me.

lobzilla commented on 2014-09-08 13:46

This is being merged back into the silo repo.

eolianoe commented on 2014-09-03 12:57

Here is a proposal for an update PKGBUILD with more functionalities : http://pastebin.com/78QBnHYM, which could be potentially merged with https://aur.archlinux.org/packages/silo-hdf5/

lobzilla commented on 2014-04-29 21:35