Bug#870205: stretch-pu: package librsb/1.2.0-rc5-3
Package: release.debian.org
Severity: normal
Tags: stretch
User: release.debian.org@packages.debian.org
Usertags: pu
Dear Release Team,
Version 1.2.0-rc5-3 of the librsb package in stretch suffers a few severe
bugs leading to numerically wrong results. These were solved in the new
upstream release 1.2.0-rc7.
Michele Martone, the upstream author, who also contributes to the Debian
package, prepared a minimal patch by backporting the fixes from version
1.2.0-rc7. This patch was attached to the report of Bug#870137.
I am attaching below the debdiff between 1.2.0-rc5-3 and the stretch
proposed-update 1.2.0-rc5-3+deb9u1. This version includes the patch
proposed by Michele Martone as well as a unit test C source file for
verifying that the fix is really implemented. I added small changes to
debian/rules and debian/clean for compiling, running and cleaning this
unit test.
Please, tell me whether this upload would be appropriate for the next
point release of stretch.
Best regards,
Raael Laboissière
-- System Information:
Debian Release: 9.0
APT prefers testing
APT policy: (650, 'testing'), (600, 'unstable'), (550, 'experimental'), (550, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.9.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.utf8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
diff -Nru librsb-1.2.0-rc5/debian/changelog librsb-1.2.0-rc5/debian/changelog
--- librsb-1.2.0-rc5/debian/changelog 2016-10-09 06:03:46.000000000 -0300
+++ librsb-1.2.0-rc5/debian/changelog 2017-07-30 18:01:10.000000000 -0300
@@ -1,3 +1,15 @@
+librsb (1.2.0-rc5-3+deb9u1) stretch; urgency=medium
+
+ * d/p/fix-numerical-computation.patch: New patch.
+ This minimal patch backports the fixes to a few severe bugs leading to
+ numerically wrong results. These bugs are fixed in the upstream
+ version 1.2.0-rc7.
+ Thanks to Michele Martone for the patch (Closes: #870137)
+ * Add unit test for numerical bug fixed in version 1.2.0-rc7.
+ Thanks to Michele Martone for the source file
+
+ -- Rafael Laboissiere <rafael@debian.org> Sun, 30 Jul 2017 18:01:10 -0300
+
librsb (1.2.0-rc5-3) unstable; urgency=medium
* d/control: Use secure URL in Vcs-Git
diff -Nru librsb-1.2.0-rc5/debian/clean librsb-1.2.0-rc5/debian/clean
--- librsb-1.2.0-rc5/debian/clean 2016-09-22 16:57:56.000000000 -0300
+++ librsb-1.2.0-rc5/debian/clean 2017-07-30 17:57:26.000000000 -0300
@@ -10,3 +10,4 @@
test.mtx
doc/html/
doc/man/man3/
+debian/rsb127_bugfix
diff -Nru librsb-1.2.0-rc5/debian/patches/fix-numerical-computation.patch librsb-1.2.0-rc5/debian/patches/fix-numerical-computation.patch
--- librsb-1.2.0-rc5/debian/patches/fix-numerical-computation.patch 1969-12-31 21:00:00.000000000 -0300
+++ librsb-1.2.0-rc5/debian/patches/fix-numerical-computation.patch 2017-07-30 18:00:11.000000000 -0300
@@ -0,0 +1,144 @@
+Description: Fix numerical computation bug
+ This is fixed in the upstream version 1.2.0-rc7.
+Author: Rafael Laboissiere <rafael@debian.org>
+Forwarded: not-needed
+Last-Update: 2017-07-30
+
+--- librsb-1.2.0-rc5.orig/rsb_krnl_bcss_macros.m4
++++ librsb-1.2.0-rc5/rsb_krnl_bcss_macros.m4
+@@ -922,9 +922,9 @@ dnl // nt: ntransposition ttranspositi
+ k=fk;
+ if(k==lk)continue;
+ j=bindx[k];
+- cacc += RSB_M4_CONJ(VA[k]*rhs[tcolsu*j*xstride],mtype,ntransposition,k_symmetry);
++ cacc += RSB_M4_CONJ(VA[k],mtype,ntransposition,k_symmetry)*rhs[tcolsu*j*xstride];
+ if(roff!=coff || (j!=i))
+- tout[(tcolsu)*(j)*ystride]+=RSB_M4_CONJ(VA[k]*bt,mtype,ttransposition,k_symmetry);
++ tout[(tcolsu)*(j)*ystride]+=RSB_M4_CONJ(VA[k],mtype,ttransposition,k_symmetry)*bt;
+ ++k;
+ dnl RSB_M4_SIMPLE_LOOP_UNROLL_2S..
+ RSB_M4_SIMPLE_LOOP_UNROLL_2S_J(`k',`LI',`fk+1',`lk-1',`dnl
+@@ -933,7 +933,7 @@ dnl
+ `const mtype b_'``''LI`'=rhs[tcolsu*(`j_'``''LI`')*xstride];
+ `const mtype a_'``''LI`'=VA[k+LI];
+ `mtype c_'``''LI`'=RSB_M4_CONJ_SYM(mtype,ttransposition,k_symmetry)( `a_'``''LI)*bt;
+-dnl `mtype c_'``''LI`'=RSB_M4_CONJ(( `a_'``''LI *bt ),mtype,transposition,k_symmetry);
++dnl `mtype c_'``''LI`'=RSB_M4_CONJ(( `a_'``''LI),mtype,transposition,k_symmetry) *bt ;
+ dnl
+ ',`dnl
+ cacc += RSB_M4_CONJ_SYM(mtype,ntransposition,k_symmetry)(`a_'``''LI)*b_``''LI;
+@@ -942,9 +942,9 @@ dnl
+ if(k<lk)
+ {
+ j=bindx[k];
+- cacc += RSB_M4_CONJ(VA[k]*rhs[trowsu*j*xstride],mtype,ntransposition,k_symmetry);
++ cacc += RSB_M4_CONJ(VA[k],mtype,ntransposition,k_symmetry)*rhs[trowsu*j*xstride];
+ if(roff!=coff || (j!=i))
+- tout[(tcolsu)*(j)*ystride]+=RSB_M4_CONJ(VA[k]*bt,mtype,ttransposition,k_symmetry);
++ tout[(tcolsu)*(j)*ystride]+=RSB_M4_CONJ(VA[k],mtype,ttransposition,k_symmetry)*bt;
+ ++k;
+ }
+ popdef(`ntransposition')dnl
+@@ -1047,7 +1047,7 @@ dnl
+ dnl Fixed for Hermitian k_symmetry.
+ dnl
+ ifelse(is_diag_d_spsv_kernel,1,`dnl
+- out[trowsu*bri]-=RSB_M4_CONJ(*a*ax_0,mtype,transposition,k_symmetry);
++ out[trowsu*bri]-=RSB_M4_CONJ(*a,mtype,transposition,k_symmetry)*ax_0;
+ ',`dnl
+ {RSB_M4_KERNEL_FUNCTION_BODY(`row',`rows',b_rows,`column',`columns',b_columns,mtype,,mop,unrolling,RSB_M4_SYMBOL_UNSYMMETRIC)}
+ ')dnl
+--- librsb-1.2.0-rc5.orig/rsb_libspblas_handle.c
++++ librsb-1.2.0-rc5/rsb_libspblas_handle.c
+@@ -1,6 +1,6 @@
+ /*
+
+-Copyright (C) 2008-2015 Michele Martone
++Copyright (C) 2008-2017 Michele Martone
+
+ This file is part of librsb.
+
+@@ -1527,9 +1527,15 @@ int rsb__BLAS_Xusget_element(blas_sparse
+ \ingroup gr_internals
+ */
+ rsb_err_t errval = RSB_ERR_NO_ERROR;
++#if 1
++ struct rsb_blas_sparse_matrix_t * bsm = NULL;
++ if( ( bsm = rsb__BLAS_matrix_retrieve(A)) != NULL && bsm->base == blas_one_base )
++ i-=1, j-=1;
++ errval = rsb__do_get_coo_element(bsm->mtxAp,v,i,j);
++#else
+ struct rsb_mtx_t * mtxAp = rsb__BLAS_inner_matrix_retrieve(A);
+-
+ errval = rsb__do_get_coo_element(mtxAp,v,i,j);
++#endif
+ return RSB_ERROR_TO_BLAS_ERROR(errval);
+ }
+
+--- librsb-1.2.0-rc5.orig/rsb_util.m4
++++ librsb-1.2.0-rc5/rsb_util.m4
+@@ -2708,6 +2708,7 @@ again`_'RSB_M4_CHOPSPACES(mtype):
+ --ti;
+ vT[ti] += vB[bi] + vC[ci];
+ ++bi;
++ ++ci;
+ ++ti;
+ ++onz;
+ }
+@@ -2715,16 +2716,16 @@ again`_'RSB_M4_CHOPSPACES(mtype):
+ t0 = ti;
+ if ( bi<nnzB && ci<nnzC && RSB_COO_GT(IB[bi],JB[bi],IC[ci],JC[ci]) )
+ {
+- IT[ti] = IB[bi];
+- JT[ti] = JB[bi];
+- vT[ti] = vB[bi] + vC[ci];
+- ++bi,++ci,++ti;
++ IT[ti] = IC[ci];
++ JT[ti] = JC[ci];
++ vT[ti] = vC[ci];
++ ++ci,++ti;
+ }
+
+ while( bi<nnzB && ci<nnzC && RSB_COO_GT(IB[bi],JB[bi],IC[ci],JC[ci]) && ti > 0 && RSB_COO_EQ(IC[ci],JC[ci],IT[ti-1],JT[ti-1]) )
+ {
+ --ti;
+- vT[ti] += vB[bi] + vC[ci];
++ vT[ti] += vC[ci];
+ ++ci;
+ ++ti;
+ ++onz;
+@@ -2733,6 +2734,8 @@ again`_'RSB_M4_CHOPSPACES(mtype):
+ if( ci < nnzC && bi < nnzB )
+ goto again`_'RSB_M4_CHOPSPACES(mtype);
+
++again`_once_'RSB_M4_CHOPSPACES(mtype):
++
+ if ( bi<nnzB && ci==nnzC )
+ {
+ IT[ti] = IB[bi];
+@@ -2761,14 +2764,14 @@ again`_'RSB_M4_CHOPSPACES(mtype):
+ while( ci<nnzC && bi==nnzB && ti > 0 && RSB_COO_EQ(IC[ci],JC[ci],IT[ti-1],JT[ti-1]) )
+ {
+ --ti;
+- IT[ti] = IC[ci];
+- JT[ti] = JC[ci];
+ vT[ti]+= vC[ci];
+ ++ci;
+ ++ti;
+ ++onz;
+ }
+
++ if( ci < nnzC || bi < nnzB )
++ goto again`_once_'RSB_M4_CHOPSPACES(mtype);
+ }
+ else
+ #endif
+@@ -2825,7 +2828,7 @@ foreach(`mtypeb',RSB_M4_TYPES,`dnl
+ mtypeb*tdst = dst;
+ ifelse(RSB_M4_AND(RSB_M4_IS_COMPLEX_TYPE(mtypeb)),1,`dnl
+ if(RSB_DOES_CONJUGATE(transA))
+- for(nzi=0;nzi<nnz;++nzi) RSB_M4_ASSIGN(mtypeb,mtypea,`tdst[nzi]',`RSB_M4_CONJ(`(mtypeb)(alpha*tsrc[nzi])',mtypeb,RSB_M4_TRANS_C,RSB_M4_SYMBOL_UNSYMMETRIC)')
++ for(nzi=0;nzi<nnz;++nzi) RSB_M4_ASSIGN(mtypeb,mtypea,`tdst[nzi]',`(mtypeb)(alpha*RSB_M4_CONJ(`tsrc[nzi]',mtypeb,RSB_M4_TRANS_C,RSB_M4_SYMBOL_UNSYMMETRIC))')
+ else
+ ')dnl
+ for(nzi=0;nzi<nnz;++nzi) RSB_M4_ASSIGN(mtypeb,mtypea,`tdst[nzi]',`(mtypeb)(alpha*tsrc[nzi])')
diff -Nru librsb-1.2.0-rc5/debian/patches/series librsb-1.2.0-rc5/debian/patches/series
--- librsb-1.2.0-rc5/debian/patches/series 2016-10-09 06:03:36.000000000 -0300
+++ librsb-1.2.0-rc5/debian/patches/series 2017-07-30 18:00:11.000000000 -0300
@@ -1,3 +1,4 @@
use-shared-lib.patch
fix-path-of-mtx-files.patch
compile-fortran-examples.patch
+fix-numerical-computation.patch
diff -Nru librsb-1.2.0-rc5/debian/rsb127_bugfix.c librsb-1.2.0-rc5/debian/rsb127_bugfix.c
--- librsb-1.2.0-rc5/debian/rsb127_bugfix.c 1969-12-31 21:00:00.000000000 -0300
+++ librsb-1.2.0-rc5/debian/rsb127_bugfix.c 2017-07-30 17:57:26.000000000 -0300
@@ -0,0 +1,59 @@
+/* This program demonstrates a bug fixed in librsb-1.2-rc7. */
+
+#include <rsb.h>
+#include <stdio.h>
+
+int main(const int argc, char * const argv[])
+{
+ rsb_err_t errval = RSB_ERR_NO_ERROR;
+ int i;
+ const int N = 2;
+ double complex x[N], y[N];
+ const double complex alpha = 1.0;
+ double complex VA[]={1,1,2};
+ int IA[]={0,0,1},JA[]={0,1,1},nnz=3;
+ struct rsb_mtx_t * mtxAp;
+ // matrix:
+ // (1,0) (1,0)
+ // (1,0) (1,0)
+ // represented as upper hermitian:
+ // (1,0) (1,0)
+ // (0,0) (1,0)
+ // multiplicand vector:
+ // (0,1)
+ // (0,0)
+ // result shall be:
+ // (0,1)
+ // (0,1)
+ errval = rsb_lib_init(RSB_NULL_INIT_OPTIONS);
+ if(errval != RSB_ERR_NO_ERROR)
+ goto err;
+ mtxAp = rsb_mtx_alloc_from_coo_begin(2, RSB_NUMERICAL_TYPE_DOUBLE_COMPLEX, N, N, RSB_FLAG_DEFAULT_STORAGE_FLAGS|RSB_FLAG_UPPER_HERMITIAN , &errval);
+ errval = rsb_mtx_set_vals(mtxAp, VA, IA, JA, nnz, RSB_FLAG_NOFLAGS);
+ if(errval != RSB_ERR_NO_ERROR)
+ goto err;
+ errval = rsb_mtx_alloc_from_coo_end(&mtxAp);
+ if(errval != RSB_ERR_NO_ERROR)
+ goto err;
+ for (i = 0; i < N; i++) x[i] = y[i] = 0.0;
+ x[0] = I;
+ errval = rsb_spmv(RSB_TRANSPOSITION_N, &alpha, mtxAp, x, 1, NULL, y, 1);
+ if(errval != RSB_ERR_NO_ERROR)
+ goto err;
+ for (i = 0; i < N; i++)
+ printf("(%g,%g)\t", creal(y[i]), cimag(y[i]));
+ printf("\n");
+ if(cimag(y[1])!=1)
+ printf("Result seems incorrect -- are you using < librsb-1.2-rc7?\n");
+ else
+ printf("Result seems correct -- are you using >= librsb-1.2-rc7?\n");
+ rsb_mtx_free(mtxAp);
+
+ errval = rsb_lib_exit(RSB_NULL_EXIT_OPTIONS);
+ if(errval != RSB_ERR_NO_ERROR)
+ goto err;
+ return 0;
+err:
+ rsb_perror(NULL,errval);
+ return -1;
+}
diff -Nru librsb-1.2.0-rc5/debian/rules librsb-1.2.0-rc5/debian/rules
--- librsb-1.2.0-rc5/debian/rules 2016-10-09 06:03:36.000000000 -0300
+++ librsb-1.2.0-rc5/debian/rules 2017-07-30 17:57:26.000000000 -0300
@@ -21,6 +21,9 @@
override_dh_auto_test:
make qtests
+ (cd debian ; \
+ gcc -o rsb127_bugfix -I.. -L../.libs -lrsb rsb127_bugfix.c ; \
+ LD_LIBRARY_PATH=../.libs ./rsb127_bugfix )
override_dh_compress:
dh_compress -X.c -X.F90
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