From 44197776e18a5a4c8e98c834a8f7b46bfe0306cc Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Tue, 31 Oct 2023 18:30:44 +0000
Subject: [PATCH 01/10] Fast seek through file

---
 yt/frontends/ramses/io_utils.pyx | 56 +++++++++++++++++++++++++-------
 1 file changed, 44 insertions(+), 12 deletions(-)

diff --git a/yt/frontends/ramses/io_utils.pyx b/yt/frontends/ramses/io_utils.pyx
index 7becee63486..3e57a79184c 100644
--- a/yt/frontends/ramses/io_utils.pyx
+++ b/yt/frontends/ramses/io_utils.pyx
@@ -14,6 +14,10 @@ ctypedef np.int32_t INT32_t
 ctypedef np.int64_t INT64_t
 ctypedef np.float64_t DOUBLE_t
 
+cdef INT32_SIZE = sizeof(np.int32_t)
+cdef INT64_SIZE = sizeof(np.int64_t)
+cdef DOUBLE_SIZE = sizeof(np.float64_t)
+
 @cython.cpow(True)
 @cython.boundscheck(False)
 @cython.wraparound(False)
@@ -134,6 +138,9 @@ cpdef read_offset(FortranFile f, INT64_t min_level, INT64_t domain_id, INT64_t n
 
     return offset, level_count
 
+cdef inline int skip_len(int Nskip, int record_len):
+    return Nskip * (record_len * DOUBLE_SIZE + INT64_SIZE)
+
 @cython.cpow(True)
 @cython.boundscheck(False)
 @cython.wraparound(False)
@@ -154,16 +161,27 @@ def fill_hydro(FortranFile f,
     cdef dict tmp
     cdef str field
     cdef INT64_t twotondim
-    cdef int ilevel, icpu, ifield, nfields, nlevels, nc, ncpu_selected
-    cdef np.ndarray[np.uint8_t, ndim=1] mask
+    cdef int ilevel, icpu, nlevels, nc, ncpu_selected, nfields_selected
 
     twotondim = 2**ndim
-    nfields = len(all_fields)
+    nfields_selected = len(fields)
 
     nlevels = offsets.shape[1]
     ncpu_selected = len(cpu_enumerator)
 
-    mask = np.array([(field in fields) for field in all_fields], dtype=np.uint8)
+    cdef np.int64_t[:] jumps = np.zeros(nfields_selected + 1, dtype=np.int64)
+    cdef int jump_len
+
+    jump_len = 0
+    j = 0
+    for i, field in enumerate(all_fields):
+        if field in fields:
+            jumps[j] = jump_len
+            j += 1
+            jump_len = 0
+        else:
+            jump_len += 1
+    jumps[j] = jump_len
 
     # Loop over levels
     for ilevel in range(nlevels):
@@ -176,19 +194,33 @@ def fill_hydro(FortranFile f,
             if offset == -1:
                 continue
             f.seek(offset)
-            tmp = {}
             # Initialize temporary data container for io
             # note: we use Fortran ordering to reflect the in-file ordering
-            for field in all_fields:
-                tmp[field] = np.empty((nc, twotondim), dtype="float64", order='F')
+            buffer = np.empty((nc, twotondim, nfields_selected), dtype="float64", order='F')
 
+            jump_len = 0
             for i in range(twotondim):
                 # Read the selected fields
-                for ifield in range(nfields):
-                    if not mask[ifield]:
-                        f.skip()
-                    else:
-                        tmp[all_fields[ifield]][:, i] = f.read_vector('d') # i-th cell
+                for j in range(nfields_selected):
+                    jump_len += jumps[j]
+                    if jump_len > 0:
+                        f.seek(skip_len(jump_len, nc), 1)
+                        jump_len = 0
+                    buffer[:, i, j] = f.read_vector('d')
+
+                jump_len += jumps[nfields_selected]
+
+            # In principle, we may be left with some fields to skip
+            # but since we're doing an absolute seek above,
+            # we don't need to do anything here
+            ## if jump_len > 0:
+            ##     f.seek(skip_len(jump_len, nc), 1)
+
+            # Alias buffer into dictionary
+            tmp = {}
+            for i, field in enumerate(fields):
+                tmp[field] = buffer[:, :, i]
+
             if ncpu_selected > 1:
                 oct_handler.fill_level_with_domain(
                     ilevel, levels, cell_inds, file_inds, domains, tr, tmp, domain=icpu+1)

From bad7f6686da2ef9044e4fbf78a76fc6a2f7df718 Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Tue, 31 Oct 2023 18:41:13 +0000
Subject: [PATCH 02/10] Make performance-critical loop C-only

---
 yt/frontends/ramses/io_utils.pyx      |  6 +++--
 yt/utilities/cython_fortran_utils.pxd |  1 +
 yt/utilities/cython_fortran_utils.pyx | 32 +++++++++++++++++++++++++++
 3 files changed, 37 insertions(+), 2 deletions(-)

diff --git a/yt/frontends/ramses/io_utils.pyx b/yt/frontends/ramses/io_utils.pyx
index 3e57a79184c..5f8fbc284f9 100644
--- a/yt/frontends/ramses/io_utils.pyx
+++ b/yt/frontends/ramses/io_utils.pyx
@@ -138,7 +138,7 @@ cpdef read_offset(FortranFile f, INT64_t min_level, INT64_t domain_id, INT64_t n
 
     return offset, level_count
 
-cdef inline int skip_len(int Nskip, int record_len):
+cdef inline int skip_len(int Nskip, int record_len) noexcept:
     return Nskip * (record_len * DOUBLE_SIZE + INT64_SIZE)
 
 @cython.cpow(True)
@@ -162,6 +162,7 @@ def fill_hydro(FortranFile f,
     cdef str field
     cdef INT64_t twotondim
     cdef int ilevel, icpu, nlevels, nc, ncpu_selected, nfields_selected
+    cdef int i, j
 
     twotondim = 2**ndim
     nfields_selected = len(fields)
@@ -171,6 +172,7 @@ def fill_hydro(FortranFile f,
 
     cdef np.int64_t[:] jumps = np.zeros(nfields_selected + 1, dtype=np.int64)
     cdef int jump_len
+    cdef np.ndarray[np.float64_t, ndim=3] buffer
 
     jump_len = 0
     j = 0
@@ -206,7 +208,7 @@ def fill_hydro(FortranFile f,
                     if jump_len > 0:
                         f.seek(skip_len(jump_len, nc), 1)
                         jump_len = 0
-                    buffer[:, i, j] = f.read_vector('d')
+                    f.read_vector_inplace('d', <void*> &buffer[0, i, j])
 
                 jump_len += jumps[nfields_selected]
 
diff --git a/yt/utilities/cython_fortran_utils.pxd b/yt/utilities/cython_fortran_utils.pxd
index ab6c2a0dc59..71c35fe1210 100644
--- a/yt/utilities/cython_fortran_utils.pxd
+++ b/yt/utilities/cython_fortran_utils.pxd
@@ -13,6 +13,7 @@ cdef class FortranFile:
     cdef INT64_t get_size(self, str dtype)
     cpdef INT32_t read_int(self) except? -1
     cpdef np.ndarray read_vector(self, str dtype)
+    cdef int read_vector_inplace(self, str dtype, void *data)
     cpdef INT64_t tell(self) except -1
     cpdef INT64_t seek(self, INT64_t pos, INT64_t whence=*) except -1
     cpdef void close(self)
diff --git a/yt/utilities/cython_fortran_utils.pyx b/yt/utilities/cython_fortran_utils.pyx
index aa26add5c16..a1edbc70f4b 100644
--- a/yt/utilities/cython_fortran_utils.pyx
+++ b/yt/utilities/cython_fortran_utils.pyx
@@ -142,6 +142,38 @@ cdef class FortranFile:
 
         return data
 
+    cdef int read_vector_inplace(self, str dtype, void *data):
+        """Reads a record from the file and return it as numpy array.
+
+        Parameters
+        ----------
+        d : data type
+            This is the datatype (from the struct module) that we should read.
+        data : void*
+            The pointer to the data to be read.
+
+        """
+        cdef INT32_t s1, s2, size
+
+        if self._closed:
+            raise ValueError("I/O operation on closed file.")
+
+        size = self.get_size(dtype)
+
+        fread(&s1, INT32_SIZE, 1, self.cfile)
+
+        # Check record is compatible with data type
+        if s1 % size != 0:
+            raise ValueError('Size obtained (%s) does not match with the expected '
+                             'size (%s) of multi-item record' % (s1, size))
+
+        fread(data, size, s1 // size, self.cfile)
+        fread(&s2, INT32_SIZE, 1, self.cfile)
+
+        if s1 != s2:
+            raise IOError('Sizes do not agree in the header and footer for '
+                          'this record - check header dtype')
+
     cpdef INT32_t read_int(self) except? -1:
         """Reads a single int32 from the file and return it.
 

From ada5ddab4b82bcb9708b7a05a3260d723a35b69d Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Tue, 31 Oct 2023 18:51:55 +0000
Subject: [PATCH 03/10] Also make reading offset faster

---
 yt/frontends/ramses/field_handlers.py |  2 +-
 yt/frontends/ramses/io_utils.pyx      | 15 ++++++++-------
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/yt/frontends/ramses/field_handlers.py b/yt/frontends/ramses/field_handlers.py
index 10860b5afd5..edd0f612f7b 100644
--- a/yt/frontends/ramses/field_handlers.py
+++ b/yt/frontends/ramses/field_handlers.py
@@ -272,7 +272,7 @@ def offset(self):
                 self.domain.domain_id,
                 self.parameters["nvar"],
                 self.domain.amr_header,
-                skip_len=nvars * 8,
+                Nskip=nvars * 8,
             )
 
         self._offset = offset
diff --git a/yt/frontends/ramses/io_utils.pyx b/yt/frontends/ramses/io_utils.pyx
index 5f8fbc284f9..831bc4e67c4 100644
--- a/yt/frontends/ramses/io_utils.pyx
+++ b/yt/frontends/ramses/io_utils.pyx
@@ -87,12 +87,16 @@ def read_amr(FortranFile f, dict headers,
 
     return max_level
 
+
+cdef inline int skip_len(int Nskip, int record_len) noexcept:
+    return Nskip * (record_len * DOUBLE_SIZE + INT64_SIZE)
+
 @cython.cpow(True)
 @cython.boundscheck(False)
 @cython.wraparound(False)
 @cython.cdivision(True)
 @cython.nonecheck(False)
-cpdef read_offset(FortranFile f, INT64_t min_level, INT64_t domain_id, INT64_t nvar, dict headers, int skip_len):
+cpdef read_offset(FortranFile f, INT64_t min_level, INT64_t domain_id, INT64_t nvar, dict headers, int Nskip):
 
     cdef np.ndarray[np.int64_t, ndim=2] offset, level_count
     cdef INT64_t ndim, twotondim, nlevelmax, n_levels, nboundary, ncpu, ncpu_and_bound
@@ -108,8 +112,8 @@ cpdef read_offset(FortranFile f, INT64_t min_level, INT64_t domain_id, INT64_t n
     ncpu_and_bound = nboundary + ncpu
     twotondim = 2**ndim
 
-    if skip_len == -1:
-        skip_len = twotondim * nvar
+    if Nskip == -1:
+        Nskip = twotondim * nvar
 
     # It goes: level, CPU, 8-variable (1 oct)
     offset = np.full((ncpu_and_bound, n_levels), -1, dtype=np.int64)
@@ -134,13 +138,10 @@ cpdef read_offset(FortranFile f, INT64_t min_level, INT64_t domain_id, INT64_t n
             if ilevel >= min_level:
                 offset_view[icpu, ilevel - min_level] = f.tell()
                 level_count_view[icpu, ilevel - min_level] = <INT64_t> file_ncache
-            f.skip(skip_len)
+            f.seek(skip_len(Nskip, file_ncache), 1)
 
     return offset, level_count
 
-cdef inline int skip_len(int Nskip, int record_len) noexcept:
-    return Nskip * (record_len * DOUBLE_SIZE + INT64_SIZE)
-
 @cython.cpow(True)
 @cython.boundscheck(False)
 @cython.wraparound(False)

From 50711d0f60d537975d30fd9d23317884b66e244e Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Tue, 31 Oct 2023 19:06:21 +0000
Subject: [PATCH 04/10] Make performance-critical functions cpdef'ed

---
 yt/geometry/oct_container.pxd | 23 +++++++++++++++++++++
 yt/geometry/oct_container.pyx | 39 ++++++++++++++++++++---------------
 2 files changed, 45 insertions(+), 17 deletions(-)

diff --git a/yt/geometry/oct_container.pxd b/yt/geometry/oct_container.pxd
index 5ac9f9318a7..3891f8fdab0 100644
--- a/yt/geometry/oct_container.pxd
+++ b/yt/geometry/oct_container.pxd
@@ -82,6 +82,29 @@ cdef class OctreeContainer:
     cdef public object fill_style
     cdef public int max_level
 
+    cpdef void fill_level(
+        self,
+        const int level,
+        const np.uint8_t[:] levels,
+        const np.uint8_t[:] cell_inds,
+        const np.int64_t[:] file_inds,
+        dict dest_fields,
+        dict source_fields,
+        np.int64_t offset = ?
+    )
+    cpdef int fill_level_with_domain(
+        self,
+        const int level,
+        const np.uint8_t[:] levels,
+        const np.uint8_t[:] cell_inds,
+        const np.int64_t[:] file_inds,
+        const np.int32_t[:] domains,
+        dict dest_fields,
+        dict source_fields,
+        const np.int32_t domain,
+        np.int64_t offset = ?
+    )
+
 cdef class SparseOctreeContainer(OctreeContainer):
     cdef OctKey *root_nodes
     cdef void *tree_root
diff --git a/yt/geometry/oct_container.pyx b/yt/geometry/oct_container.pyx
index 7d3118cb252..4b09d360e51 100644
--- a/yt/geometry/oct_container.pyx
+++ b/yt/geometry/oct_container.pyx
@@ -742,12 +742,16 @@ cdef class OctreeContainer:
     @cython.boundscheck(False)
     @cython.wraparound(False)
     @cython.cdivision(True)
-    def fill_level(self, int level,
-                   np.ndarray[np.uint8_t, ndim=1] levels,
-                   np.ndarray[np.uint8_t, ndim=1] cell_inds,
-                   np.ndarray[np.int64_t, ndim=1] file_inds,
-                   dest_fields, source_fields,
-                   np.int64_t offset = 0):
+    cpdef void fill_level(
+        self,
+        const int level,
+        const np.uint8_t[:] levels,
+        const np.uint8_t[:] cell_inds,
+        const np.int64_t[:] file_inds,
+        dict dest_fields,
+        dict source_fields,
+        np.int64_t offset = 0
+    ):
         cdef np.ndarray[np.float64_t, ndim=2] source
         cdef np.ndarray[np.float64_t, ndim=1] dest
         cdef int i, lvl
@@ -824,17 +828,18 @@ cdef class OctreeContainer:
     @cython.boundscheck(False)
     @cython.wraparound(False)
     @cython.cdivision(True)
-    def fill_level_with_domain(
-                   self, int level,
-                   np.uint8_t[:] levels,
-                   np.uint8_t[:] cell_inds,
-                   np.int64_t[:] file_inds,
-                   np.int32_t[:] domains,
-                   dict dest_fields,
-                   dict source_fields,
-                   np.int32_t domain,
-                   np.int64_t offset = 0
-                   ):
+    cpdef int fill_level_with_domain(
+        self,
+        const int level,
+        const np.uint8_t[:] levels,
+        const np.uint8_t[:] cell_inds,
+        const np.int64_t[:] file_inds,
+        const np.int32_t[:] domains,
+        dict dest_fields,
+        dict source_fields,
+        const np.int32_t domain,
+        np.int64_t offset = 0
+    ):
         """Similar to fill_level but accepts a domain argument.
 
         This is particularly useful for frontends that have buffer zones at CPU boundaries.

From 253f0ead1bf9581071e37413669b9372fa7f3b3e Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Wed, 1 Nov 2023 11:04:48 +0000
Subject: [PATCH 05/10] Fix the docstring

---
 yt/utilities/cython_fortran_utils.pyx | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/yt/utilities/cython_fortran_utils.pyx b/yt/utilities/cython_fortran_utils.pyx
index a1edbc70f4b..fc2008fc419 100644
--- a/yt/utilities/cython_fortran_utils.pyx
+++ b/yt/utilities/cython_fortran_utils.pyx
@@ -143,15 +143,15 @@ cdef class FortranFile:
         return data
 
     cdef int read_vector_inplace(self, str dtype, void *data):
-        """Reads a record from the file and return it as numpy array.
+        """Reads a record from the file.
 
         Parameters
         ----------
         d : data type
             This is the datatype (from the struct module) that we should read.
         data : void*
-            The pointer to the data to be read.
-
+            The pointer where to store the data.
+            It should be preallocated and have the correct size.
         """
         cdef INT32_t s1, s2, size
 

From 57fef2fd35af61d1738ad2458c87502f4150ee21 Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Wed, 1 Nov 2023 11:27:36 +0000
Subject: [PATCH 06/10] Avoid repetitive allocations

---
 yt/frontends/ramses/io_utils.pyx | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/yt/frontends/ramses/io_utils.pyx b/yt/frontends/ramses/io_utils.pyx
index 831bc4e67c4..76b59d1cc47 100644
--- a/yt/frontends/ramses/io_utils.pyx
+++ b/yt/frontends/ramses/io_utils.pyx
@@ -14,9 +14,9 @@ ctypedef np.int32_t INT32_t
 ctypedef np.int64_t INT64_t
 ctypedef np.float64_t DOUBLE_t
 
-cdef INT32_SIZE = sizeof(np.int32_t)
-cdef INT64_SIZE = sizeof(np.int64_t)
-cdef DOUBLE_SIZE = sizeof(np.float64_t)
+cdef int INT32_SIZE = sizeof(np.int32_t)
+cdef int INT64_SIZE = sizeof(np.int64_t)
+cdef int DOUBLE_SIZE = sizeof(np.float64_t)
 
 @cython.cpow(True)
 @cython.boundscheck(False)
@@ -163,7 +163,7 @@ def fill_hydro(FortranFile f,
     cdef str field
     cdef INT64_t twotondim
     cdef int ilevel, icpu, nlevels, nc, ncpu_selected, nfields_selected
-    cdef int i, j
+    cdef int i, j, ii
 
     twotondim = 2**ndim
     nfields_selected = len(fields)
@@ -171,7 +171,9 @@ def fill_hydro(FortranFile f,
     nlevels = offsets.shape[1]
     ncpu_selected = len(cpu_enumerator)
 
-    cdef np.int64_t[:] jumps = np.zeros(nfields_selected + 1, dtype=np.int64)
+    cdef np.int64_t[::1] cpu_list = np.asarray(cpu_enumerator, dtype=np.int64)
+
+    cdef np.int64_t[::1] jumps = np.zeros(nfields_selected + 1, dtype=np.int64)
     cdef int jump_len
     cdef np.ndarray[np.float64_t, ndim=3] buffer
 
@@ -186,10 +188,12 @@ def fill_hydro(FortranFile f,
             jump_len += 1
     jumps[j] = jump_len
 
+    cdef int nc_largest = 0
     # Loop over levels
     for ilevel in range(nlevels):
         # Loop over cpu domains
-        for icpu in cpu_enumerator:
+        for ii in range(ncpu_selected):
+            icpu = cpu_list[ii]
             nc = level_count[icpu, ilevel]
             if nc == 0:
                 continue
@@ -199,7 +203,9 @@ def fill_hydro(FortranFile f,
             f.seek(offset)
             # Initialize temporary data container for io
             # note: we use Fortran ordering to reflect the in-file ordering
-            buffer = np.empty((nc, twotondim, nfields_selected), dtype="float64", order='F')
+            if nc > nc_largest:
+                nc_largest = nc
+                buffer = np.empty((nc, twotondim, nfields_selected), dtype="float64", order='F')
 
             jump_len = 0
             for i in range(twotondim):

From d33e2b130c47a2325bbc7342fde9b84bba905403 Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Wed, 1 Nov 2023 17:23:19 +0000
Subject: [PATCH 07/10] Make comment more obvious

---
 yt/frontends/ramses/io_utils.pyx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/yt/frontends/ramses/io_utils.pyx b/yt/frontends/ramses/io_utils.pyx
index 76b59d1cc47..cb58ad98c57 100644
--- a/yt/frontends/ramses/io_utils.pyx
+++ b/yt/frontends/ramses/io_utils.pyx
@@ -220,8 +220,8 @@ def fill_hydro(FortranFile f,
                 jump_len += jumps[nfields_selected]
 
             # In principle, we may be left with some fields to skip
-            # but since we're doing an absolute seek above,
-            # we don't need to do anything here
+            # but since we're doing an absolute seek at the beginning of
+            # the loop on CPUs, we can spare one seek here
             ## if jump_len > 0:
             ##     f.seek(skip_len(jump_len, nc), 1)
 

From a16bda2a47ea639dfdb76233a3e4204164e8e236 Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Wed, 1 Nov 2023 17:31:24 +0000
Subject: [PATCH 08/10] Making the skip_len nogil, just to be safe

---
 yt/frontends/ramses/io_utils.pyx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/yt/frontends/ramses/io_utils.pyx b/yt/frontends/ramses/io_utils.pyx
index cb58ad98c57..335176eff2e 100644
--- a/yt/frontends/ramses/io_utils.pyx
+++ b/yt/frontends/ramses/io_utils.pyx
@@ -88,7 +88,7 @@ def read_amr(FortranFile f, dict headers,
     return max_level
 
 
-cdef inline int skip_len(int Nskip, int record_len) noexcept:
+cdef inline int skip_len(int Nskip, int record_len) noexcept nogil:
     return Nskip * (record_len * DOUBLE_SIZE + INT64_SIZE)
 
 @cython.cpow(True)

From b3eef0d1aae7adb3bb9ade1159bba39ce0995cb9 Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Fri, 3 Nov 2023 14:37:47 +0000
Subject: [PATCH 09/10] Preallocate given maximal size

---
 yt/frontends/ramses/io_utils.pyx | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/yt/frontends/ramses/io_utils.pyx b/yt/frontends/ramses/io_utils.pyx
index 335176eff2e..579f36ec439 100644
--- a/yt/frontends/ramses/io_utils.pyx
+++ b/yt/frontends/ramses/io_utils.pyx
@@ -188,7 +188,7 @@ def fill_hydro(FortranFile f,
             jump_len += 1
     jumps[j] = jump_len
 
-    cdef int nc_largest = 0
+    buffer = np.empty((level_count.max(), twotondim, nfields_selected), dtype="float64", order='F')
     # Loop over levels
     for ilevel in range(nlevels):
         # Loop over cpu domains
@@ -201,11 +201,6 @@ def fill_hydro(FortranFile f,
             if offset == -1:
                 continue
             f.seek(offset)
-            # Initialize temporary data container for io
-            # note: we use Fortran ordering to reflect the in-file ordering
-            if nc > nc_largest:
-                nc_largest = nc
-                buffer = np.empty((nc, twotondim, nfields_selected), dtype="float64", order='F')
 
             jump_len = 0
             for i in range(twotondim):

From 7a953bcbecd63cddf04c4e6ec927bf72948fea9b Mon Sep 17 00:00:00 2001
From: Corentin Cadiou <corentin.cadiou@cphyc.me>
Date: Fri, 3 Nov 2023 14:50:47 +0000
Subject: [PATCH 10/10] Spare the first jump

---
 yt/frontends/ramses/io_utils.pyx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/yt/frontends/ramses/io_utils.pyx b/yt/frontends/ramses/io_utils.pyx
index 579f36ec439..9dc749e1400 100644
--- a/yt/frontends/ramses/io_utils.pyx
+++ b/yt/frontends/ramses/io_utils.pyx
@@ -187,6 +187,7 @@ def fill_hydro(FortranFile f,
         else:
             jump_len += 1
     jumps[j] = jump_len
+    cdef int first_field_index = jumps[0]
 
     buffer = np.empty((level_count.max(), twotondim, nfields_selected), dtype="float64", order='F')
     # Loop over levels
@@ -200,9 +201,11 @@ def fill_hydro(FortranFile f,
             offset = offsets[icpu, ilevel]
             if offset == -1:
                 continue
-            f.seek(offset)
+            f.seek(offset + skip_len(first_field_index, nc))
 
-            jump_len = 0
+            # We have already skipped the first fields (if any)
+            # so we "rewind" (this will cancel the first seek)
+            jump_len = -first_field_index
             for i in range(twotondim):
                 # Read the selected fields
                 for j in range(nfields_selected):