atlas: remove

atlas is broken and can apparently be removed.

Fixes #49594

pkgs/applications/science/math/giac/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, fetchpatch, texlive, bison, flex, liblapackWithoutAtlas
+{ stdenv, fetchurl, fetchpatch, texlive, bison, flex, liblapack
 , gmp, mpfr, pari, ntl, gsl, blas, mpfi
 , readline, gettext, libpng, libao, gfortran, perl
 , enableGUI ? false, libGLU_combined ? null, xorg ? null, fltk ? null
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
     # gfortran.cc default output contains static libraries compiled without -fPIC
     # we want libgfortran.so.3 instead
     (stdenv.lib.getLib gfortran.cc)
-    liblapackWithoutAtlas
+    liblapack
   ] ++ stdenv.lib.optionals enableGUI [
     libGLU_combined fltk xorg.libX11
   ];

pkgs/applications/science/physics/xfitter/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, apfel, apfelgrid, applgrid, blas, gfortran, lhapdf, liblapackWithoutAtlas, libyaml, lynx, mela, root5, qcdnum, which }:
+{ stdenv, fetchurl, apfel, apfelgrid, applgrid, blas, gfortran, lhapdf, liblapack, libyaml, lynx, mela, root5, qcdnum, which }:
 
 stdenv.mkDerivation rec {
   name = "xfitter-${version}";
@@ -34,7 +34,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ gfortran which ];
   buildInputs =
-    [ apfel apfelgrid applgrid blas lhapdf liblapackWithoutAtlas mela root5 qcdnum ]
+    [ apfel apfelgrid applgrid blas lhapdf liblapack mela root5 qcdnum ]
     # pdf2yaml requires fmemopen and open_memstream which are not readily available on Darwin
     ++ stdenv.lib.optional (!stdenv.isDarwin) libyaml
     ;

pkgs/development/libraries/science/math/atlas/default.nix

@@ -1,126 +0,0 @@
-{ stdenv, fetchurl, gfortran, tolerateCpuTimingInaccuracy ? true, shared ? false
-, cpuConfig ? if stdenv.isi686 then "-b 32 -A 12 -V 1" else "-b 64 -A 14 -V 384"
-, cacheEdge ? "262144"
-, threads ? "0"
-, liblapack, withLapack
-}:
-
-# Atlas detects the CPU and optimizes its build accordingly. This is great when
-# the code is run on the same machine that built the binary, but in case of a
-# central build farm like Hydra, this feature is dangerous because the code may
-# be generated utilizing fancy features that users who download the binary
-# cannot execute.
-#
-# To avoid these issues, the build is configured using the 'cpuConfig'
-# parameter. Upstream recommends these defaults for distributions:
-#
-#   | x86 CPU                                     | x86_64 CPU             |
-#   |---------------------------------------------+------------------------|
-#   | -b 32                                       | -b 64                  |
-#   | -A 12  (x86x87)                             | -A 14 (x86SSE2)        |
-#   | -V 1 (No SIMD)                              | -V 384 (SSE1 and SSE2) |
-#
-# These defaults should give consistent performance across machines.
-# Performance will be substantially lower than an optimized build, but a build
-# optimized for one machine will give even worse performance on others. If you
-# are a serious user of Atlas (e.g., you write code that uses it) you should
-# compile an optimized version for each of your machines.
-#
-# The parameter 'cacheEdge' sets the L2 cache per core (in bytes). Setting this
-# parameter reduces build time because some tests to detect the L2 cache size
-# will not be run. It will also reduce impurity; different build nodes on Hydra
-# may have different L2 cache sizes, but fixing the L2 cache size should
-# account for that. This also makes the performance of binary substitutes more
-# consistent.
-#
-# The -V flags can change with each release as new instruction sets are added
-# because upstream thinks it's a good idea to add entries at the start of an
-# enum, rather than the end. If the build suddenly fails with messages about
-# missing instruction sets, you may need to poke around in the source a bit.
-#
-# Upstream recommends the x86x87/x86SSE2 architectures for generic x86/x86_64
-# for distribution builds. Additionally, we set 'cacheEdge' to reduce impurity.
-# Otherwise, the cache parameters will be detected by timing which will be
-# highly variable on Hydra.
-
-let
-  inherit (stdenv.lib) optional optionalString;
-  # Don't upgrade until https://github.com/math-atlas/math-atlas/issues/44
-  # is resolved.
-  version = "3.10.3";
-in
-
-stdenv.mkDerivation {
-  name = "atlas${optionalString withLapack "-with-lapack"}-${version}";
-
-  src = fetchurl {
-    url = "mirror://sourceforge/math-atlas/atlas${version}.tar.bz2";
-    sha256 = "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216";
-  };
-
-  buildInputs = [ gfortran ];
-
-  # Atlas aborts the build if it detects that some kind of CPU frequency
-  # scaling is active on the build machine because that feature offsets the
-  # performance timings. We ignore that check, however, because with binaries
-  # being pre-built on Hydra those timings aren't accurate for the local
-  # machine in the first place.
-  patches = optional tolerateCpuTimingInaccuracy ./disable-timing-accuracy-check.patch
-    ++ optional stdenv.isDarwin ./tmpdir.patch;
-
-  hardeningDisable = [ "format" ];
-
-  # Configure outside of the source directory.
-  preConfigure = ''
-    mkdir build
-    cd build
-    configureScript=../configure
-  '';
-
-  # * -t 0 disables use of multi-threading. It's not quite clear what the
-  #   consequences of that setting are and whether it's necessary or not.
-  configureFlags = [
-    "-t ${threads}"
-    cpuConfig
-  ] ++ optional shared "--shared"
-    ++ optional withLapack "--with-netlib-lapack-tarfile=${liblapack.src}";
-
-  postConfigure = ''
-    if [[ -n "${cacheEdge}" ]]; then
-      echo '#define CacheEdge ${cacheEdge}' >> include/atlas_cacheedge.h
-      echo '#define CacheEdge ${cacheEdge}' >> include/atlas_tcacheedge.h
-    fi
-  '';
-
-  doCheck = true;
-
-  postInstall = ''
-    # Avoid name collision with the real lapack (ATLAS only builds a partial
-    # lapack unless withLapack = true).
-    if ${if withLapack then "false" else "true"}; then
-      mv $out/lib/liblapack.a $out/lib/liblapack_atlas.a
-    fi
-  '';
-
-  # 1. /buildATLAS/build/bin/ATLrun.sh: multiple segfaults.
-  # 2. "atlas does its own parallel builds"
-  enableParallelBuilding = false;
-
-  meta = {
-    homepage = http://math-atlas.sourceforge.net/;
-    description = "Automatically Tuned Linear Algebra Software (ATLAS)";
-    license = stdenv.lib.licenses.bsd3;
-    broken = stdenv.isDarwin;  # test when updating to >=3.10.3
-    platforms = stdenv.lib.platforms.unix;
-
-    longDescription = ''
-      The ATLAS (Automatically Tuned Linear Algebra Software) project is an
-      ongoing research effort focusing on applying empirical techniques in
-      order to provide portable performance. At present, it provides C and
-      Fortran77 interfaces to a portably efficient BLAS implementation, as well
-      as a few routines from LAPACK.
-    '';
-
-    maintainers = with stdenv.lib.maintainers; [ ttuegel ];
-  };
-}

pkgs/development/libraries/science/math/atlas/disable-timing-accuracy-check.patch

@@ -1,22 +0,0 @@
-diff -ubr ATLAS-orig/CONFIG/src/config.c ATLAS/CONFIG/src/config.c
---- ATLAS-orig/CONFIG/src/config.c	2013-02-06 11:23:47.078036878 +0100
-+++ ATLAS/CONFIG/src/config.c	2013-02-06 11:24:16.481120888 +0100
-@@ -711,17 +711,7 @@
- 
- int ProbeCPUThrottle(int verb, char *targarg, enum OSTYPE OS, enum ASMDIA asmb)
- {
--   int i, iret;
--   char *ln;
--   i = strlen(targarg) + 22 + 12;
--   ln = malloc(i*sizeof(char));
--   assert(ln);
--   sprintf(ln, "%s -O %d -s %d -t", targarg, OS, asmb);
--   iret = GetIntProbe(verb, ln, "arch", "CPU THROTTLE", 0);
--   free(ln);
--   if (iret) printf("CPU Throttling apparently enabled!\n");
--   else printf("Cannot detect CPU throttling.\n");
--   return(iret);
-+   return 0;
- }
- 
- char *NewAppendedString_SFLAG(char *old, char *flag, char *str)

pkgs/development/libraries/science/math/atlas/tmpdir.patch

@@ -1,276 +0,0 @@
-diff --git a/CONFIG/ARCHS/negflt.c b/CONFIG/ARCHS/negflt.c
-index e5b7871..d45e387 100644
---- a/CONFIG/ARCHS/negflt.c
-+++ b/CONFIG/ARCHS/negflt.c
-@@ -239,7 +239,7 @@ void NegFile(char *fnam, int N, int *cols)
-    FILE *fpin, *fpout;
-    WORDS *wp0, *wp;
- 
--   tnam = tmpnam(NULL);
-+   tnam = tempnam(NULL, NULL);
-    fpin = fopen(fnam, "r");
-    assert(fpin);
-    fpout = fopen(tnam, "w");
-diff --git a/CONFIG/include/atlas_sys.h b/CONFIG/include/atlas_sys.h
-index b83a749..8902d38 100644
---- a/CONFIG/include/atlas_sys.h
-+++ b/CONFIG/include/atlas_sys.h
-@@ -216,12 +216,13 @@ static char *ATL_fgets_CWS(char *sout, int *plen, FILE *fpin)
- 
- static char *ATL_tmpnam(void)
- {
--   static char tnam[L_tmpnam];
-+   static char *tnam;
-    static char FirstTime=1;
-    if (FirstTime)
-    {
-       FirstTime = 0;
--      assert(tmpnam(tnam));
-+      tnam = tempnam(NULL, NULL);
-+      assert(tnam);
-    }
-    return(tnam);
- }
-diff --git a/bin/atlas_install.c b/bin/atlas_install.c
-index 2753cbf..e49cc3e 100644
---- a/bin/atlas_install.c
-+++ b/bin/atlas_install.c
-@@ -662,7 +662,8 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
- {
-    const char TR[2] = {'N','T'};
-    char prec[4] = {'d', 's', 'z', 'c'}, pre, upre, *typ;
--   char ln[1024], tnam[256], ln2[512], ln3[512], fnam[128];
-+   char ln[1024], ln2[512], ln3[512], fnam[128];
-+   char *tnam;
-    char *mulinst, *peakstr, *peakstr2;
-    int nprec=4;
-    int iL1, lat, muladd, maused, latuse, lbnreg;
-@@ -681,7 +682,7 @@ void GoToTown(int ARCHDEF, int L1DEF, int TuneLA)
-    fpsum = fopen("INSTALL_LOG/SUMMARY.LOG", "a");
-    ATL_Cassert(fpsum, "OPENING INSTALL_LOG/SUMMARY.LOG", NULL);
- 
--   ATL_Cassert(tmpnam(tnam), "GETTING TEMPFILE", NULL);
-+   ATL_Cassert((tnam = tempnam(NULL, NULL)), "GETTING TEMPFILE", NULL);
- 
-    if (L1DEF)
-    {
-diff --git a/bin/extract.c b/bin/extract.c
-index 7a5a926..53fb8bf 100644
---- a/bin/extract.c
-+++ b/bin/extract.c
-@@ -3378,7 +3378,7 @@ void PushProc0(EXTENV *EE, EXTPROC **basep, EXTPROC **myfuncs, char *ln)
-    pp->argnams = KillWord(wp, wp);
-    pp->nargs = CountWords(pp->argnams);
- 
--   cp = tmpnam(NULL);
-+   cp = tempnam(NULL, NULL);
-    if (cp == NULL) ExtErr(EE, "Out of tmpnams!!!");
-    i = Wstrlen(cp) + 1;
-    pp->FileNam = malloc(i*sizeof(char));
-diff --git a/include/atlas_mvtesttime.h b/include/atlas_mvtesttime.h
-index 9147fcb..ab6a99f 100644
---- a/include/atlas_mvtesttime.h
-+++ b/include/atlas_mvtesttime.h
-@@ -105,14 +105,15 @@ static int MVKernelFailsTest
-    char ln[4096];
-    char *sp;
-    int i, lda0;
--   static char outnam[L_tmpnam];
-+   static char* outnam;
-    static int FirstTime=1;
- 
-    if (FirstTime)
-    {
- 
-       FirstTime = 0;
--      assert(tmpnam(outnam));
-+      outnam = tempnam(NULL, NULL);
-+      assert(outnam);
-    }
- /*
-  * If the file is generated, call generator to create it
-@@ -221,14 +222,15 @@ static double TimeMVKernel
-    char ln[2048], resf[256], *sp;
-    double *dp, mf;
-    int i, align = pre2size(pre);
--   static char outnam[L_tmpnam];
-+   static char* outnam;
-    static int FirstTime=1;
- 
-    if (FirstTime)
-    {
- 
-       FirstTime = 0;
--      assert(tmpnam(outnam));
-+      outnam = tempnam(NULL, NULL);
-+      assert(outnam);
-    }
- /*
-  * If the file is generated, call generator to create it
-diff --git a/include/atlas_r1testtime.h b/include/atlas_r1testtime.h
-index b33213a..f27ee25 100644
---- a/include/atlas_r1testtime.h
-+++ b/include/atlas_r1testtime.h
-@@ -76,14 +76,15 @@ static int R1KernelFailsTest
-    char ln[4096];
-    char *sp;
-    int i, lda0;
--   static char outnam[L_tmpnam];
-+   static char* outnam;
-    static int FirstTime=1;
- 
-    if (FirstTime)
-    {
- 
-       FirstTime = 0;
--      assert(tmpnam(outnam));
-+      outnam = tempnam(NULL, NULL);
-+      assert(outnam);
-    }
- /*
-  * If the file is generated, call generator to create it
-@@ -187,14 +188,15 @@ static double TimeR1Kernel
-    char ln[2048], resf[256], *sp;
-    double *dp, mf;
-    int i, align = pre2size(pre);
--   static char outnam[L_tmpnam];
-+   static char* outnam;
-    static int FirstTime=1;
- 
-    if (FirstTime)
-    {
- 
-       FirstTime = 0;
--      assert(tmpnam(outnam));
-+      outnam = tempnam(NULL, NULL);
-+      assert(outnam);
-    }
- /*
-  * If the file is generated, call generator to create it
-diff --git a/include/atlas_r2testtime.h b/include/atlas_r2testtime.h
-index facc66d..c638dce 100644
---- a/include/atlas_r2testtime.h
-+++ b/include/atlas_r2testtime.h
-@@ -76,14 +76,15 @@ static int R2KernelFailsTest
-    char ln[4096];
-    char *sp;
-    int i, lda0;
--   static char outnam[L_tmpnam];
-+   static char* outnam;
-    static int FirstTime=1;
- 
-    if (FirstTime)
-    {
- 
-       FirstTime = 0;
--      assert(tmpnam(outnam));
-+      outnam = tempnam(NULL, NULL);
-+      assert(outnam);
-    }
- /*
-  * If the file is generated, call generator to create it
-@@ -187,14 +188,15 @@ static double TimeR2Kernel
-    char ln[2048], resf[256], *sp;
-    double *dp, mf;
-    int i, align = pre2size(pre);
--   static char outnam[L_tmpnam];
-+   static char* outnam;
-    static int FirstTime=1;
- 
-    if (FirstTime)
-    {
- 
-       FirstTime = 0;
--      assert(tmpnam(outnam));
-+      outnam = tempnam(NULL, NULL);
-+      assert(outnam);
-    }
- /*
-  * If the file is generated, call generator to create it
-diff --git a/include/atlas_sys.h b/include/atlas_sys.h
-index b83a749..b3f88d2 100644
---- a/include/atlas_sys.h
-+++ b/include/atlas_sys.h
-@@ -216,12 +216,13 @@ static char *ATL_fgets_CWS(char *sout, int *plen, FILE *fpin)
- 
- static char *ATL_tmpnam(void)
- {
--   static char tnam[L_tmpnam];
-+   static char* tnam;
-    static char FirstTime=1;
-    if (FirstTime)
-    {
-       FirstTime = 0;
--      assert(tmpnam(tnam));
-+      tnam = tempnam(NULL, NULL);
-+      assert(tnam);
-    }
-    return(tnam);
- }
-diff --git a/tune/blas/gemm/usercomb.c b/tune/blas/gemm/usercomb.c
-index 59a7cd4..eb3eb05 100644
---- a/tune/blas/gemm/usercomb.c
-+++ b/tune/blas/gemm/usercomb.c
-@@ -138,11 +138,13 @@ int GetUserCase(char pre, int icase, int *iflag, int *mb, int *nb, int *kb,
- 
- void CombineFiles(char *fout, int nfiles, char **fnams)
- {
--   char tnam[256], ln[512];
-+   char ln[512];
-+   char *tnam;
-    int i, j, n, nn;
-    FILE *fpout, *fpin;
- 
--   assert(tmpnam(tnam));
-+   tnam = tempnam(NULL, NULL);
-+   assert(tnam);
-    for (n=i=0; i < nfiles; i++) n += NumUserCases0(fnams[i]);
- 
-    fpout = fopen(tnam, "w");
-diff --git a/tune/blas/gemm/userflag.c b/tune/blas/gemm/userflag.c
-index c3983e4..b7dd70b 100644
---- a/tune/blas/gemm/userflag.c
-+++ b/tune/blas/gemm/userflag.c
-@@ -139,8 +139,8 @@ int GetUserCase(char pre, int icase, int *iflag, int *mb, int *nb, int *kb,
- 
- void GoGetThem(char *infile, char *outfile)
- {
--   char ln[512], ln2[512], tnam[256], MCC[256], MMFLAGS[256];
--   char *chkfile = "FlagCheck.c", *sp, *sp2;
-+   char ln[512], ln2[512], MCC[256], MMFLAGS[256];
-+   char *chkfile = "FlagCheck.c", *sp, *sp2, *tnam;
-    FILE *fpin, *fpout;
-    int i, j, n, nmin=0, good;
-    int wass;
-@@ -152,7 +152,8 @@ void GoGetThem(char *infile, char *outfile)
-    n = NumUserCases0(infile);
-    fpin = fopen(infile, "r");
-    assert(fpin);
--   assert(tmpnam(tnam));
-+   tnam = tempnam(NULL, NULL);
-+   assert(tnam);
-    fpout = fopen(tnam, "w");
-    assert(fpout);
-    assert(fgets(ln, 512, fpin));
-diff --git a/tune/sysinfo/emit_buildinfo.c b/tune/sysinfo/emit_buildinfo.c
-index 309c06a..3feaea7 100644
---- a/tune/sysinfo/emit_buildinfo.c
-+++ b/tune/sysinfo/emit_buildinfo.c
-@@ -41,14 +41,15 @@ static char SMCVERS[LNLEN], DMCVERS[LNLEN], SKCVERS[LNLEN], DKCVERS[LNLEN];
- static char UNAM[64], DATE[128];
- char *CmndResults(char *cmnd)
- {
--   static char tnam[128];
-+   static char* tnam;
-    static int FirstTime=1;
-    char ln[512];
- 
-    if (FirstTime)
-    {
-       FirstTime = 0;
--      assert(tmpnam(tnam));
-+      tnam = tempnam(NULL, NULL);
-+      assert(tnam);
-    }
-    sprintf(ln, "%s > %s\n", cmnd, tnam);
-    fprintf(stderr, "system: %s", ln);

pkgs/development/libraries/science/math/liblapack/default.nix

@@ -4,12 +4,9 @@
   gfortran,
   cmake,
   python2,
-  atlas ? null,
   shared ? false
 }:
 let
-  atlasMaybeShared = if atlas != null then atlas.override { inherit shared; }
-                     else null;
   usedLibExtension = if shared then ".so" else ".a";
   inherit (stdenv.lib) optional optionals;
   version = "3.8.0";
@@ -22,7 +19,6 @@ stdenv.mkDerivation rec {
     sha256 = "1xmwi2mqmipvg950gb0rhgprcps8gy8sjm8ic9rgy2qjlv22rcny";
   };
 
-  propagatedBuildInputs = [ atlasMaybeShared ];
   buildInputs = [ gfortran cmake ];
   nativeBuildInputs = [ python2 ];
 
@@ -30,15 +26,7 @@ stdenv.mkDerivation rec {
     "-DUSE_OPTIMIZED_BLAS=ON"
     "-DCMAKE_Fortran_FLAGS=-fPIC"
   ]
-  ++ (optionals (atlas != null) [
-    "-DBLAS_ATLAS_f77blas_LIBRARY=${atlasMaybeShared}/lib/libf77blas${usedLibExtension}"
-    "-DBLAS_ATLAS_atlas_LIBRARY=${atlasMaybeShared}/lib/libatlas${usedLibExtension}"
-  ])
-  ++ (optional shared "-DBUILD_SHARED_LIBS=ON")
-  # If we're on darwin, CMake will automatically detect impure paths. This switch
-  # prevents that.
-  ++ (optional stdenv.isDarwin "-DCMAKE_OSX_SYSROOT:PATH=''")
-  ;
+  ++ (optional shared "-DBUILD_SHARED_LIBS=ON");
 
   doCheck = ! shared;
 
@@ -48,10 +36,6 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  passthru = {
-    blas = atlas;
-  };
-
   meta = with stdenv.lib; {
     inherit version;
     description = "Linear Algebra PACKage";

pkgs/top-level/all-packages.nix

@@ -16101,9 +16101,7 @@ with pkgs;
 
   cpp_ethereum = callPackage ../applications/misc/cpp-ethereum { };
 
-  csdp = callPackage ../applications/science/math/csdp {
-    liblapack = liblapackWithoutAtlas;
-  };
+  csdp = callPackage ../applications/science/math/csdp { };
 
   ctop = callPackage ../tools/system/ctop { };
 
@@ -21171,16 +21169,6 @@ with pkgs;
 
   arpack = callPackage ../development/libraries/science/math/arpack { };
 
-  atlas = callPackage ../development/libraries/science/math/atlas {
-    # The build process measures CPU capabilities and optimizes the
-    # library to perform best on that particular machine. That is a
-    # great feature, but it's of limited use with pre-built binaries
-    # coming from a central build farm.
-    tolerateCpuTimingInaccuracy = true;
-    liblapack = liblapackWithoutAtlas;
-    withLapack = false;
-  };
-
   blas = callPackage ../development/libraries/science/math/blas { };
 
   brial = callPackage ../development/libraries/science/math/brial { };
@@ -21203,13 +21191,7 @@ with pkgs;
 
   libhomfly = callPackage ../development/libraries/science/math/libhomfly { };
 
-  # We have essentially 4 permutations of liblapack: version 3.4.1 or 3.5.0,
-  # and with or without atlas as a dependency. The default `liblapack` is 3.4.1
-  # with atlas. Atlas, when built with liblapack as a dependency, uses 3.5.0
-  # without atlas. Etc.
   liblapack = callPackage ../development/libraries/science/math/liblapack {};
-  liblapackWithoutAtlas = liblapackWithAtlas.override { atlas = null; };
-  liblapackWithAtlas = liblapack;
 
   liblbfgs = callPackage ../development/libraries/science/math/liblbfgs { };
 
@@ -21276,9 +21258,7 @@ with pkgs;
 
   QuadProgpp = callPackage ../development/libraries/science/math/QuadProgpp { };
 
-  scs = callPackage ../development/libraries/science/math/scs {
-    liblapack = liblapackWithoutAtlas;
-  };
+  scs = callPackage ../development/libraries/science/math/scs { };
 
   sage = callPackage ../applications/science/math/sage {
     nixpkgs = pkgs;

pkgs/top-level/release-small.nix

@@ -18,7 +18,6 @@ with import ./release-lib.nix { inherit supportedSystems; };
 
   aspell = all;
   at = linux;
-  atlas = linux;
   autoconf = all;
   automake = all;
   avahi = unix; # Cygwin builds fail