mysql innodb 引擎下ibd文件过大的问题排查记录

最新推荐文章于 2025-04-27 13:07:06 发布

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#mysql #数据库 #java

问题描述：

mysql版本：8.0.12 表存储引擎为innodb

数据库某张表中数据只有100条左右数据，但表文件（ibd文件）占用磁盘空间却达到了1.8G。

该表的表结构如下：

CREATE TABLE `k8s_node_status` (
  `id` int(11) NOT NULL AUTO_INCREMENT,
  `master_ip` varchar(255)  NOT NULL ,
  `node_name` varchar(255)  DEFAULT NULL,
  `node_ip` varchar(255)  DEFAULT NULL,
  `node_status` tinyint(5) DEFAULT NULL ,
  `update_time` timestamp NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP ,
  `create_time` timestamp NULL DEFAULT CURRENT_TIMESTAMP,
  `delete_flag` tinyint(1) DEFAULT '0' ,
  `reason` varchar(100)  DEFAULT NULL ,
  `message` varchar(4000)  DEFAULT NULL,
  `labels` text ,
  `annotations` text ,
  `taints` tinyint(1) DEFAULT NULL ,
  `cpu_total` decimal(16,3) DEFAULT NULL ,
  `memory_total` decimal(16,3) DEFAULT NULL ,
  `fs_total` decimal(16,3) DEFAULT NULL ,
  `version` varchar(32) DEFAULT NULL ,
  `yaml_content` text CHARACTER SET utf8 COLLATE utf8_general_ci,
  `master` tinyint(1) DEFAULT NULL ,
  `allow_pods` int(8) DEFAULT NULL ,
  `uid` varchar(64)  DEFAULT NULL,
  `start_time` timestamp NULL DEFAULT NULL ,
  `delete_time` timestamp NULL DEFAULT NULL ,
  PRIMARY KEY (`id`) USING BTREE,
  UNIQUE KEY `unique_uid_deleteflag_masterip` (`uid`,`delete_flag`,`master_ip`) USING BTREE,
  KEY `idx_nodename` (`node_name`) USING BTREE,
  KEY `idx_nodeip` (`node_ip`) USING BTREE,
  KEY `idx_masterip` (`master_ip`) USING BTREE
) ENGINE=InnoDB AUTO_INCREMENT=100 DEFAULT CHARSET=utf8 ROW_FORMAT=DYNAMIC;

原因猜想1：数据页空缺造成的页空洞？

innodb存储引擎中，表数据是以B+树的数据结构存储的，树的每个叶子节点存储一行数据，而这些节点又是存储在数据页（page）上，innodb引擎默认数据页的大小是16Kb，多个连续的页又会组成区(extent)。其存储结构如下图：

数据在B+树的实例如下：

我们要删掉 R4 这个记录，InnoDB 引擎只会把 R4 这个记录标记为删除。如果之后要再插入一个 ID 在 300 和 600 之间的记录时，可能会复用这个位置。但是，磁盘文件的大小并不会缩小。如果删除page A上的所有数据，那么这个页会被标记为可复用。

不止删除数据会造成页空洞，插入数据时，若主键值不是自增而是随机的，那么就有可能触发页分裂而造成页空洞。

更新数据时，若更新了索引值，那么会删除旧数据，插入一条新数据，也会造成页空洞。例如将R4记录的id从500更新为800，那么会将R4记录标记为删除，同时新增一条记录。

若没有更新索引值，只是更新某个字段，那么如果更新后的记录的长度（占用字节数）比原记录长，且原记录前后无空闲位置，那么会执行delete+update操作，可能会造成页空洞。（这个场景有待严格的验证）

结合以上可能造成数据页空洞的场景，我们的表并没有频繁删除/新增记录的操作，这一点通过自增主键可以看出来，该表的自增主键的值仅为100（AUTO_INCREMENT=100），因此不会是删除和新增数据造成页空洞。那么那就有可能是更新造成的页空洞。

为进一步确定是否是频繁更新造成的页空洞，我们通过查看TABLES表数据，其中DATA_FREE字段表示被分配但未使用的字节数大小，这个值为4194304=4M，这部分空间是可以被分配的，包括上面所说的记录被删除后造成的空白页。显然页空洞并不是造成数据文件过大的原因。

原因猜想2:text频繁更新引起？

再次看我们的表结构，其中有3个text字段，分别是labels、annotations、yaml_content。其中labels、annotations字段实际存储的字符长度在100～500这个范围，不算太大。而yaml_content字段保存了yaml文件，字符长度竟达到的10000+的长度。而这个字段又是频繁变动更新的。因此猜测是yaml_content频繁更新引起的ibd文件过大。

在此之前需要先了解一下，text字段是如何存储的，innodb数据页大小为16KB=16384byte，也就是最多存16384个字节。每个页存储的记录是有限制的，最多存16KB/2-200行的记录，也就是7992行。最少存2行的记录。那么对于超出16384个字符长度的行记录该如何存储呢？对于Compact行格式，有以下结论：

结论一：当行长度发生溢出时，数据存放在页类型为Uncompress BLOB页（溢出页）中
结论二：对于行溢出数据，其保留数据的前768个字节的前缀数据，之后偏移量指向溢出页
结论三：为保证一个页中至少有2条行记录，单条行记录阈值长度为8098，若行长度超过这个阈值，则会发生行溢出，数据会保存在溢出页中，数据页只保留前缀768个字节。
结论四：当InnoDB更新存储在溢出页中的大字段时，将不会在原来的位置更新。而是会在写一个新值到一个新的空间，并且不会删除旧的值。

注：Dynamic行格式，列存储是否放到off-page页，主要取决于行大小，他会把行中最长的一列放到off-page，直到数据页能存放下两行。TEXT或BLOB列<=40bytes时总是存在于数据页。这种方式可以避免compact那样把太多的大列值放到B-tree Node（数据页中只存放20个字节的指针，实际的数据存放在Off Page中，之前的Compact 和 Redundant 两种格式会存放768个字前缀字节）。

实际上我们的k8s_node_status表中yaml_content字段长度在10000+字符，且频繁更新，触发了上面结论4，导致表文件（.ibd文件）持续膨胀。

我们在测试环境复制一张k8s_node_status表，此时表中无数据，然后插入一条数据如下：

INSERT INTO `test`.`k8s_node_status`(`id`, `master_ip`, `node_name`, `node_ip`, `node_status`, `update_time`, `create_time`, `delete_flag`, `reason`, `message`, `labels`, `annotations`, `taints`, `cpu_total`, `memory_total`, `fs_total`, `version`, `yaml_content`, `master`, `allow_pods`, `uid`, `start_time`, `delete_time`) VALUES (9, 'test_default_default', '10.10.103.219-slave', '10.10.103.219', 0, '2022-03-24 08:57:52', '2022-01-18 11:42:43', 0, '', '', 'os: linux', 'kubeadm.alpha.kubernetes.io/cri-socket: /var/run/dockershim.sock,management.cattle.io/pod-limits: {\"cpu\":\"6782m\",\"memory\":\"14756Mi\"},management.cattle.io/pod-requests: {\"cpu\":\"6718m\",\"memory\":\"9722Mi\",\"pods\":\"21\"},node.alpha.kubernetes.io/ttl: 0,projectcalico.org/IPv4Address: 10.10.103.219/24,projectcalico.org/IPv4IPIPTunnelAddr: 192.168.24.64,volumes.kubernetes.io/controller-managed-attach-detach: true', 0, 8.000, 16657936384.000, 157696397312.000, '26815075', 'apiVersion: v1', 0, 110, '8f5111b0-1edc-4e7c-bd22-11733693642b', '2022-01-07 03:08:13', NULL);

这条数据中的text字段设置为几个字符，总字符数在1000左右，这时分析表文件（ibd文件），可以看到如下结果：

分析：插入一条数据时，表文件中只有4个数据页<B-tree Node>,没有溢出页。符合上述结论3

然后我们插入一条“正常”数据，这条数据的yaml_content字段长度达到10000个字符，再分析ibd文件如下：

INSERT INTO `test`.`k8s_node_status`(`id`, `master_ip`, `node_name`, `node_ip`, `node_status`, `update_time`, `create_time`, `delete_flag`, `reason`, `message`, `labels`, `annotations`, `taints`, `cpu_total`, `memory_total`, `fs_total`, `version`, `yaml_content`, `master`, `allow_pods`, `uid`, `start_time`, `delete_time`) VALUES (13, 'test_default_default', '10.10.103.221-slave', '10.10.103.221', 0, '2022-03-24 08:58:57', '2022-01-18 11:42:43', 0, '', '', 'beta.kubernetes.io/arch: amd64,beta.kubernetes.io/os: linux,kubernetes.io/arch: amd64,kubernetes.io/hostname: 10.10.103.221-slave,kubernetes.io/os: linux', 'kubeadm.alpha.kubernetes.io/cri-socket: /var/run/dockershim.sock,management.cattle.io/pod-limits: {\"cpu\":\"4882m\",\"memory\":\"6589Mi\"},management.cattle.io/pod-requests: {\"cpu\":\"4718m\",\"memory\":\"5895Mi\",\"pods\":\"12\"},node.alpha.kubernetes.io/ttl: 0,projectcalico.org/IPv4Address: 10.10.103.221/24,projectcalico.org/IPv4IPIPTunnelAddr: 192.168.68.192,volumes.kubernetes.io/controller-managed-attach-detach: true', 0, 8.000, 16657932288.000, 157696397312.000, '26815328', 'apiVersion: v1\nkind: Node\nmetadata:\n  annotations:\n    kubeadm.alpha.kubernetes.io/cri-socket: /var/run/dockershim.sock\n    management.cattle.io/pod-limits: \'{\"cpu\":\"4882m\",\"memory\":\"6589Mi\"}\'\n    management.cattle.io/pod-requests: \'{\"cpu\":\"4718m\",\"memory\":\"5895Mi\",\"pods\":\"12\"}\'\n    node.alpha.kubernetes.io/ttl: \'0\'\n    projectcalico.org/IPv4Address: 10.10.103.221/24\n    projectcalico.org/IPv4IPIPTunnelAddr: 192.168.68.192\n    volumes.kubernetes.io/controller-managed-attach-detach: \'true\'\n  creationTimestamp: \'2022-01-07T03:08:02.000+08:00\'\n  labels:\n    beta.kubernetes.io/arch: amd64\n    beta.kubernetes.io/os: linux\n    kubernetes.io/arch: amd64\n    kubernetes.io/hostname: 10.10.103.221-slave\n    kubernetes.io/os: linux\n  managedFields:\n  - apiVersion: v1\n    fieldsType: FieldsV1\n    fieldsV1:\n      f:metadata:\n        f:annotations:\n          f:kubeadm.alpha.kubernetes.io/cri-socket: {}\n    manager: kubeadm\n    operation: Update\n    time: \'2022-01-07T03:08:03.000+08:00\'\n  - apiVersion: v1\n    fieldsType: FieldsV1\n    fieldsV1:\n      f:metadata:\n        f:annotations:\n          f:projectcalico.org/IPv4Address: {}\n          f:projectcalico.org/IPv4IPIPTunnelAddr: {}\n      f:status:\n        f:conditions:\n          k:{\"type\":\"NetworkUnavailable\"}:\n            .: {}\n            f:lastHeartbeatTime: {}\n            f:lastTransitionTime: {}\n            f:message: {}\n            f:reason: {}\n            f:status: {}\n            f:type: {}\n    manager: calico-node\n    operation: Update\n    time: \'2022-01-07T03:09:23.000+08:00\'\n  - apiVersion: v1\n    fieldsType: FieldsV1\n    fieldsV1:\n      f:metadata:\n        f:annotations:\n          f:management.cattle.io/pod-limits: {}\n          f:management.cattle.io/pod-requests: {}\n    manager: agent\n    operation: Update\n    time: \'2022-03-10T09:43:22.000+08:00\'\n  - apiVersion: v1\n    fieldsType: FieldsV1\n    fieldsV1:\n      f:metadata:\n        f:annotations:\n          f:node.alpha.kubernetes.io/ttl: {}\n      f:spec:\n        f:podCIDR: {}\n        f:podCIDRs:\n          .: {}\n          v:\"192.168.3.0/24\": {}\n    manager: kube-controller-manager\n    operation: Update\n    time: \'2022-03-22T09:47:38.000+08:00\'\n  - apiVersion: v1\n    fieldsType: FieldsV1\n    fieldsV1:\n      f:metadata:\n        f:annotations:\n          .: {}\n          f:volumes.kubernetes.io/controller-managed-attach-detach: {}\n        f:labels:\n          .: {}\n          f:beta.kubernetes.io/arch: {}\n          f:beta.kubernetes.io/os: {}\n          f:kubernetes.io/arch: {}\n          f:kubernetes.io/hostname: {}\n          f:kubernetes.io/os: {}\n      f:status:\n        f:addresses:\n          .: {}\n          k:{\"type\":\"Hostname\"}:\n            .: {}\n            f:address: {}\n            f:type: {}\n          k:{\"type\":\"InternalIP\"}:\n            .: {}\n            f:address: {}\n            f:type: {}\n        f:allocatable:\n          .: {}\n          f:cpu: {}\n          f:ephemeral-storage: {}\n          f:hugepages-1Gi: {}\n          f:hugepages-2Mi: {}\n          f:memory: {}\n          f:pods: {}\n        f:capacity:\n          .: {}\n          f:cpu: {}\n          f:ephemeral-storage: {}\n          f:hugepages-1Gi: {}\n          f:hugepages-2Mi: {}\n          f:memory: {}\n          f:pods: {}\n        f:conditions:\n          .: {}\n          k:{\"type\":\"DiskPressure\"}:\n            .: {}\n            f:lastHeartbeatTime: {}\n            f:lastTransitionTime: {}\n            f:message: {}\n            f:reason: {}\n            f:status: {}\n            f:type: {}\n          k:{\"type\":\"MemoryPressure\"}:\n            .: {}\n            f:lastHeartbeatTime: {}\n            f:lastTransitionTime: {}\n            f:message: {}\n            f:reason: {}\n            f:status: {}\n            f:type: {}\n          k:{\"type\":\"PIDPressure\"}:\n            .: {}\n            f:lastHeartbeatTime: {}\n            f:lastTransitionTime: {}\n            f:message: {}\n            f:reason: {}\n            f:status: {}\n            f:type: {}\n          k:{\"type\":\"Ready\"}:\n            .: {}\n            f:lastHeartbeatTime: {}\n            f:lastTransitionTime: {}\n            f:message: {}\n            f:reason: {}\n            f:status: {}\n            f:type: {}\n        f:daemonEndpoints:\n          f:kubeletEndpoint:\n            f:Port: {}\n        f:images: {}\n        f:nodeInfo:\n          f:architecture: {}\n          f:bootID: {}\n          f:containerRuntimeVersion: {}\n          f:kernelVersion: {}\n          f:kubeProxyVersion: {}\n          f:kubeletVersion: {}\n          f:machineID: {}\n          f:operatingSystem: {}\n          f:osImage: {}\n          f:systemUUID: {}\n    manager: kubelet\n    operation: Update\n    time: \'2022-03-22T09:47:59.000+08:00\'\n  name: 10.10.103.221-slave\n  resourceVersion: \'26815328\'\n  selfLink: /api/v1/nodes/10.10.103.221-slave\n  uid: c8cac3c8-e229-40dc-93e5-219a372fc80e\nspec:\n  podCIDR: 192.168.3.0/24\n  podCIDRs:\n  - 192.168.3.0/24\nstatus:\n  addresses:\n  - type: InternalIP\n    address: 10.10.103.221\n  - type: Hostname\n    address: 10.10.103.221-slave\n  allocatable:\n    cpu: \'8\'\n    ephemeral-storage: \'140969826890\'\n    hugepages-1Gi: \'0\'\n    hugepages-2Mi: \'0\'\n    memory: 16165112Ki\n    pods: \'110\'\n  capacity:\n    cpu: \'8\'\n    ephemeral-storage: 152962052Ki\n    hugepages-1Gi: \'0\'\n    hugepages-2Mi: \'0\'\n    memory: 16267512Ki\n    pods: \'110\'\n  conditions:\n  - type: NetworkUnavailable\n    lastHeartbeatTime: \'2022-03-22T09:46:31.000+08:00\'\n    lastTransitionTime: \'2022-03-22T09:46:31.000+08:00\'\n    message: Calico is running on this node\n    reason: CalicoIsUp\n    status: \'False\'\n  - type: MemoryPressure\n    lastHeartbeatTime: \'2022-03-24T08:56:50.000+08:00\'\n    lastTransitionTime: \'2022-03-22T09:45:55.000+08:00\'\n    message: kubelet has sufficient memory available\n    reason: KubeletHasSufficientMemory\n    status: \'False\'\n  - type: DiskPressure\n    lastHeartbeatTime: \'2022-03-24T08:56:50.000+08:00\'\n    lastTransitionTime: \'2022-03-22T09:45:55.000+08:00\'\n    message: kubelet has no disk pressure\n    reason: KubeletHasNoDiskPressure\n    status: \'False\'\n  - type: PIDPressure\n    lastHeartbeatTime: \'2022-03-24T08:56:50.000+08:00\'\n    lastTransitionTime: \'2022-03-22T09:45:55.000+08:00\'\n    message: kubelet has sufficient PID available\n    reason: KubeletHasSufficientPID\n    status: \'False\'\n  - type: Ready\n    lastHeartbeatTime: \'2022-03-24T08:56:50.000+08:00\'\n    lastTransitionTime: \'2022-03-22T09:45:55.000+08:00\'\n    message: kubelet is posting ready status\n    reason: KubeletReady\n    status: \'True\'\n  daemonEndpoints:\n    kubeletEndpoint:\n      port: 10250\n  images:\n  - names:\n    - 10.1.11.205/test-tool/myjmeter@sha256:08f8e98cdb364567d59f76b67c8c4879d0963eacc558b7e958d4b91b4fedd9a3\n    - 10.10.102.120:8443/testapp/myjmeter@sha256:08f8e98cdb364567d59f76b67c8c4879d0963eacc558b7e958d4b91b4fedd9a3\n    - 10.1.11.205/test-tool/myjmeter:v1.0\n    - 10.10.102.120:8443/testapp/myjmeter:v1.0\n    sizeBytes: 842714693\n  - names:\n    - 10.1.11.205/k8s-deploy/bookdemo@sha256:e80a8011e56092ea1ac19f622984ff985e3d5ef7d7025b779743222a2eb0c8ab\n    - 10.1.11.205/k8s-deploy/bookdemo:v5\n    sizeBytes: 840693868\n  - names:\n    - 10.10.102.213:8443/cloudnevro-test/nephele@sha256:e53ccbb3397ce2da422d5b5644f178c3b65aacded64cdc9aeb997eb63689fbcd\n    - 10.10.102.213:8443/cloudnevro-test/nephele:v1.0.0\n    sizeBytes: 773951646\n  - names:\n    - 10.10.102.213:8443/cloudnevro-jxjk/nephele@sha256:c8a728f32113a22a2becf7b89b916de6d79dcfab2c51f43a75c4bf284b1f86c5\n    - 10.10.102.213:8443/cloudnevro-jxjk/nephele:v1.0.0\n    sizeBytes: 773943383\n  - names:\n    - 10.10.102.213:8443/cloudnevro-jxjk/nephele@sha256:8a8fd140e074a2a5da3ba64250a93cbb49e03830ace5562fed6d29ecd26a26f1\n    sizeBytes: 773937443\n  - names:\n    - 10.10.102.213:8443/cloudnevro-jxjk/nephele@sha256:d6155d7d8db24b7b2e0a65052cd27b00bbc89c78ad4fc426bb694d45f2b2c187\n    sizeBytes: 773927434\n  - names:\n    - 10.1.11.205/k8s-deploy-test2/nephele@sha256:8d345345366ed39c55b125eb4a343c375266b79e19608ee6d2221c0f380ca4b4\n    sizeBytes: 772415391\n  - names:\n    - 10.1.11.205/k8s-deploy-test2/nephele@sha256:a0e9754459b2733cf7514aa0c0d318933f3335ca58b4a7153bb0f312b1a2ea47\n    - 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