Re: [igraph] Compiling igraph with the Intel compilers

[Tamás Nepusz]

For the record: we have managed to resolve the issue with the Intel compilers, 
so the 0.6 tree should compile with icc from revision 3000 onwards. Similarly, 
the first revision in the development (0.7) tree that supports icc is revision 
3043.

Those who do not want to check out the full source tree and wish to patch the 
last released version of igraph instead should cherrypick the following two 
patches only:

http://bazaar.launchpad.net/~igraph/igraph/0.6-main/revision/2989
http://bazaar.launchpad.net/~igraph/igraph/0.6-main/revision/3000

All the best,
Tamas

On 31 Oct 2012, at 14:46, Malcolm Tobias <address@hidden> wrote:

> I'm attempting to install igraph 0.6-3 using the Intel 12.1 compilers.
> I've encountered this error:
> foreign-gml-parser.c(971): error: expression must be a pointer to a complete 
> object type
> which appears to be a known bug:
> http://lists.nongnu.org/archive/html/igraph-help/2012-06/msg00048.html
> and the fix is to add:
> char* stpcpy(char* s1, const char* s2) {
>     char* result = strcpy(s1, s2);
>     return result + strlen(s1);
> }
> This resolves the error message, but then I found I needed to apply it to:
> foreign-lgl-parser.c
> foreign-ncol-parser.c
> foreign-pajek-parser.c
> While this fixes the compilation of the individual files, I'm getting a 
> link-time error:
> icpc -shared -L/export/intel/Compiler/12.1/lib/intel64/ -o igraph.so 
> DensityGrid.o DensityGrid_3d.o NetDataTypes.o NetRoutines.o adjlist.o amd_1.o 
> amd_2.o amd_aat.o amd_control.o amd_defaults.o amd_dump.o amd_info.o 
> amd_order.o amd_post_tree.o amd_postorder.o amd_preprocess.o amd_valid.o 
> arpack.o array.o atlas.o attributes.o basic_query.o bfgs.o bigint.o bignum.o 
> bipartite.o blas.o bliss.o bliss_eqrefhash.o bliss_graph.o bliss_heap.o 
> bliss_orbit.o bliss_partition.o bliss_timer.o bliss_utils.o cattributes.o 
> centrality.o cliques.o clustertool.o cocitation.o cohesive_blocks.o colamd.o 
> community.o complex.o components.o conversion.o cores.o cs_add.o cs_amd.o 
> cs_chol.o cs_cholsol.o cs_compress.o cs_counts.o cs_cumsum.o cs_dfs.o 
> cs_dmperm.o cs_droptol.o cs_dropzeros.o cs_dupl.o cs_entry.o cs_ereach.o 
> cs_etree.o cs_fkeep.o cs_gaxpy.o cs_happly.o cs_house.o cs_ipvec.o cs_leaf.o 
> cs_load.o cs_lsolve.o cs_ltsolve.o cs_lu.o cs_lusol.o cs_malloc.o 
> cs_maxtrans.o cs_multiply.o cs_norm.o cs_permute.o cs_pinv.o cs_post.o 
> cs_print.o cs_pvec.o cs_qr.o cs_qrsol.o cs_randperm.o cs_reach.o cs_scatter.o 
> cs_scc.o cs_schol.o cs_spsolve.o cs_sqr.o cs_symperm.o cs_tdfs.o 
> cs_transpose.o cs_updown.o cs_usolve.o cs_util.o cs_utsolve.o decomposition.o 
> dgetv0.o distances.o dlaqrb.o dmout.o dnaitr.o dnapps.o dnaup2.o dnaupd.o 
> dnconv.o dneigh.o dneupd.o dngets.o dqueue.o drl_graph.o drl_graph_3d.o 
> drl_layout.o drl_layout_3d.o drl_parse.o dsaitr.o dsapps.o dsaup2.o dsaupd.o 
> dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o dsortc.o dsortr.o dstatn.o 
> dstats.o dstqrb.o dvout.o eigen.o error.o evolver_cit.o f2c_dummy.o 
> fast_community.o feedback_arc_set.o flow.o foreign-dl-lexer.o 
> foreign-dl-parser.o foreign-gml-lexer.o foreign-gml-parser.o 
> foreign-graphml.o foreign-lgl-lexer.o foreign-lgl-parser.o 
> foreign-ncol-lexer.o foreign-ncol-parser.o foreign-pajek-lexer.o 
> foreign-pajek-parser.o foreign.o forestfire.o fortran_intrinsics.o games.o 
> gengraph_box_list.o gengraph_degree_sequence.o gengraph_graph_molloy_hash.o 
> gengraph_graph_molloy_optimized.o gengraph_mr-connected.o gengraph_powerlaw.o 
> gengraph_random.o glpapi01.o glpapi02.o glpapi03.o glpapi04.o glpapi05.o 
> glpapi06.o glpapi07.o glpapi08.o glpapi09.o glpapi10.o glpapi11.o glpapi12.o 
> glpapi13.o glpapi14.o glpapi15.o glpapi16.o glpapi17.o glpapi18.o glpapi19.o 
> glpavl.o glpbfd.o glpbfx.o glpcpx.o glpdmp.o glpdmx.o glpenv01.o glpenv02.o 
> glpenv03.o glpenv04.o glpenv05.o glpenv06.o glpenv07.o glpenv08.o glpfhv.o 
> glpgmp.o glphbm.o glpini01.o glpini02.o glpios01.o glpios02.o glpios03.o 
> glpios04.o glpios05.o glpios06.o glpios07.o glpios08.o glpios09.o glpios10.o 
> glpios11.o glpios12.o glpipm.o glpk_support.o glplib01.o glplib02.o 
> glplib03.o glplpf.o glplpx01.o glplpx02.o glplpx03.o glpluf.o glplux.o 
> glpmat.o glpmpl01.o glpmpl02.o glpmpl03.o glpmpl04.o glpmpl05.o glpmpl06.o 
> glpmps.o glpnet01.o glpnet02.o glpnet03.o glpnet04.o glpnet05.o glpnet06.o 
> glpnet07.o glpnet08.o glpnet09.o glpnpp01.o glpnpp02.o glpnpp03.o glpnpp04.o 
> glpnpp05.o glpqmd.o glprgr.o glprng01.o glprng02.o glpscf.o glpscl.o glpsdf.o 
> glpspm.o glpspx01.o glpspx02.o glpsql.o glpssx01.o glpssx02.o glptsp.o 
> gml_tree.o heap.o igraph_buckets.o igraph_estack.o igraph_fixed_vectorlist.o 
> igraph_grid.o igraph_hashtable.o igraph_heap.o igraph_hrg.o 
> igraph_hrg_types.o igraph_marked_queue.o igraph_psumtree.o igraph_set.o 
> igraph_stack.o igraph_strvector.o igraph_trie.o infomap.o infomap_FlowGraph.o 
> infomap_Greedy.o infomap_Node.o interrupt.o iterators.o ivout.o lapack.o 
> layout.o matching.o math.o matrix.o memory.o microscopic_update.o mixing.o 
> motifs.o operators.o optimal_modularity.o other.o pottsmodel_2.o progress.o 
> qsort.o qsort_r.o random.o revolver_cit.o revolver_grow.o revolver_ml_cit.o 
> rinterface.o scg.o scg_approximate_methods.o scg_exact_scg.o scg_kmeans.o 
> scg_optimal_method.o scg_utils.o second.o separators.o spanning_trees.o 
> sparsemat.o spectral_properties.o spmatrix.o st-cuts.o statusbar.o 
> structural_properties.o structure_generators.o sugiyama.o topology.o 
> type_indexededgelist.o types.o vector.o vector_ptr.o version.o visitors.o 
> walktrap.o walktrap_communities.o walktrap_graph.o walktrap_heap.o zeroin.o 
> -lxml2 -lz -lm -lgmp -lifport -lifcore -limf -lsvml -lm -lipgo -lirc 
> -lpthread -lirc_s -ldl -L/export/intel/Compiler/12.1/mkl/lib/intel64/ 
> -lmkl_intel_lp64 -lmkl_sequential -lmkl_lapack95_lp64 -lmkl_core -lifport 
> -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
> foreign-lgl-parser.o: In function `stpcpy':
> /tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-lgl-parser.y:63: 
> multiple definition of `stpcpy'
> foreign-gml-parser.o:/tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-gml-parser.y:65:
>  first defined here
> foreign-ncol-parser.o: In function `stpcpy':
> /tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-ncol-parser.y:65: 
> multiple definition of `stpcpy'
> foreign-gml-parser.o:/tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-gml-parser.y:65:
>  first defined here
> foreign-pajek-parser.o: In function `stpcpy':
> /tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-pajek-parser.y:67: 
> multiple definition of `stpcpy'
> foreign-gml-parser.o:/tmp/Rtmpp3Ocy4/R.INSTALL5871ca99a65/igraph/src/foreign-gml-parser.y:65:
>  first defined here
> make: *** [igraph.so] Error 1
> ERROR: compilation failed for package ‘igraph’
> * removing ‘/export/R-2.15.2/lib64/R/library/igraph’
> Any suggestions?
> Malcolm
> -- 
> Malcolm Tobias
> 314.362.1594
> _______________________________________________
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